Molecular Cell Article - Linköping University · site for p97. Unique to gp78 is a high-afﬁnity binding site for its cognate E2, Ube2g2. This Ube2g2-binding region (G2BR) is required

Molecular Cell

Article

Allosteric Activation of E2-RING Finger-MediatedUbiquitylation by a Structurally DefinedSpecific E2-Binding Region of gp78Ranabir Das,1 Jennifer Mariano,2 Yien Che Tsai,2,4 Ravi C. Kalathur,3,4 Zlatka Kostova,2 Jess Li,1 Sergey G. Tarasov,1

Robert L. McFeeters,1 Amanda S. Altieri,1 Xinhua Ji,3 R. Andrew Byrd,1,* and Allan M. Weissman2,*1Structural Biophysics Laboratory2Laboratory of Protein Dynamics and Signaling3Macromolecular Crystallography Laboratory

Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA4These authors contributed equally to this work

*Correspondence: [email protected] (R.A.B.), [email protected] (A.M.W.)DOI 10.1016/j.molcel.2009.05.010

SUMMARY

The activity of RING finger ubiquitin ligases (E3) isdependent on their ability to facilitate transfer ofubiquitin from ubiquitin-conjugating enzymes (E2)to substrates. The G2BR domain within the E3 gp78binds selectively and with high affinity to the E2Ube2g2. Through structural and functional analyses,we determine that this occurs on a region of Ube2g2distinct from binding sites for ubiquitin-activatingenzyme (E1) and RING fingers. Binding to the G2BRresults in conformational changes in Ube2g2 thataffect ubiquitin loading. The Ube2g2:G2BR interac-tion also causes an �50-fold increase in affinitybetween the E2 and RING finger. This results in mark-edly increased ubiquitylation by Ube2g2 and thegp78 RING finger. The significance of this G2BReffect is underscored by enhanced ubiquitylationobserved when Ube2g2 is paired with other RINGfinger E3s. These findings uncover a mechanismwhereby allosteric effects on an E2 enhance E2-RING finger interactions and, consequently, ubiqui-tylation.

INTRODUCTION

Ubiquitylation occurs as the result of a hierarchical multienzyme

process. Ubiquitin-activating enzyme (E1) activates ubiquitin,

forming a thiolester linkage between the active site Cys of E1

and the C terminus of ubiquitin. Ubiquitin is transferred to the

conserved active site Cys of ubiquitin-conjugating enzymes

(E2), of which there are more than 30 in mammals. E2s bind to

specific ubiquitin-protein ligases (E3s), which mediate the trans-

fer of ubiquitin to primary amines on substrates or to growing

chains of ubiquitin (polyubiquitin or multiubiquitin). In many

cases, the E3s also undergo auto- or self-ubiquitylation.

There are more than 500 E3s in mammals that can be divided

into two major classes. The HECT E3s include �30 E3s and are

674 Molecular Cell 34, 674–685, June 26, 2009 ª2009 Elsevier Inc.

characterized by a conserved 350 amino acid catalytic domain.

HECT E3s are catalytic intermediates in substrate ubiquitylation

as a consequence of the transthiolation of ubiquitin from bound

E2 to their conserved catalytic Cys (Fang and Weissman, 2004).

RING finger and RING finger-like E3s collectively represent the

large majority of E3s. The RING finger is a compact Zn-binding

domain of 40 to 100 amino acids. These domains generally

bind E2s with low affinity and do not form catalytic intermediates

with ubiquitin. It is generally believed that RING fingers either

position E2�Ub to facilitate transfer to substrates or function

as allosteric activators of E2�Ub (Lorick et al., 2005; Ozkan

et al., 2005). Binding sites on E2s for RING fingers, HECT

domains, and E1 all overlap. Therefore, E2s must dissociate

from ligase domains to reload with ubiquitin (Huang et al.,

2005; Eletr et al., 2005). Interestingly, there are a few examples

in which other regions, either within a multisubunit ubiquitin

ligase complex or a single subunit E3, bind specific E2s through

generally uncharacterized interactions (Madura et al., 1993; Ha-

takeyama et al., 1997; Wu et al., 2002; Biederer et al., 1997; Chen

et al., 2006). This could increase the availability of E2�Ub and

theoretically allow for reloading of E2 with ubiquitin without

dissociation from the E3.

Ubiquitylation and proteasomal degradation perform critical

functions in degradation of misfolded, unassembled, and highly

regulated proteins from the endoplasmic reticulum (ER). ER-

associated degradation (ERAD) is a multistep, highly coordi-

nated process (Nakatsukasa and Brodsky, 2008). In mammals,

there are at least five known ER membrane-spanning ERAD

E3s. Among these is gp78, also known as the human tumor au-

tocrine motility factor receptor (AMFR). gp78 is implicated in

degradation of T cell antigen receptor subunits, regulatory

proteins in lipid metabolism (Kostova et al., 2007), CFTRD508

(Morito et al., 2008), and the metastasis suppressor KAI1

(CD82) (Tsai et al., 2007).

gp78 has a complex domain structure for a single subunit E3.

In addition to its RING finger, it has at least three more C-terminal

domains in its extended cytoplasmic tail (Figure 1A). Each of

these is implicated in ubiquitylation and degradation of ERAD

substrates. They include a ubiquitin-binding CUE (coupling of

ubiquitin conjugation to ERAD) domain and a C-terminal binding

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Molecular Cell

gp78 Ube2g2-Binding Region: Structure and Function

Figure 1. The gp78 G2BR and Its Interactions with Ube2g2 by NMR

(A) Schematic representation of gp78 in the ER membrane (left). To the right is a linear representation of gp78 cytoplasmic tail with amino acids (corresponding to

the entire human gp78) indicated. Peptides used in this study corresponding to the G2BR, specific mutations/truncations, and a scrambled (Scr) peptide control

are shown below. Mutations are indicated in lowercase.

(B) Overlay of 15N-HSQC NMR spectra of Ube2g2 in free (red) and G2BR-bound (blue) form.

(C) The contact residues observed in an intermolecular NOESY spectrum of Ube2g2:G2BR are painted blue on the free Ube2g2 structure (PDB entry 2CYX).

Region of E1 and E3 binding based on other E2-E3 pairs is indicated by the bracket. The active site Cys (C89) is in red.

(D) 15N-HSQC of isotopically labeled G2BR in free form (red) and bound to Ube2g2 (blue).

site for p97. Unique to gp78 is a high-affinity binding site for its

cognate E2, Ube2g2. This Ube2g2-binding region (G2BR) is

required for the function of gp78 in cells (Chen et al., 2006).

We now report that the G2BR binds Ube2g2 through an

extended interface distinct from sites of RING finger and E1

binding. This results in subtle changes in the Ube2g2 core that

are manifested in functional alterations in loading with ubiquitin

and a marked increase in affinity for the gp78 RING finger, which

is reflected in enhanced ubiquitylation.

RESULTS

The G2BR Is a High-Affinity Binding Site for Ube2g2To evaluate the interaction between the gp78 G2BR (Figure 1A)

and Ube2g2, we employed isothermal titration calorimetry (ITC)

(Figure S1 available online). This confirmed the direct, high-

affinity interaction of Ube2g2 with a 27 amino acid G2BR

peptide. The 1:1 complex of E2 and G2BR has a dissociation

constant (Kd) of 21 (± 4) nM (Table 1). The reaction is exothermic,

and the significant free energy change (DG = �43.72 kJ mol�1)

implies a very stable complex. The decrease in entropy reveals

that part of the complex is losing some degree of freedom and

is likely folding into a regular structure.

‘‘Backside Binding’’ to Ube2g2 Induces G2BR FoldingTo identify the binding surface between Ube2g2 and G2BR, we

examined the interaction by monitoring the NMR spectra of each

molecule independently. First, the Ube2g2 preparation was vali-

dated by confirming the resonance assignments for Ube2g2

compared to a previous study (Briggman et al., 2005). A

secondary structure analysis based on chemical shifts (Wishart

and Sykes, 1994) combined with distance information from

a 15N-edited NOESY-HSQC spectrum confirmed that our

Ube2g2 preparation matched the reported crystal structure

(Arai et al., 2006). Titration of G2BR into isotopically labeled

Ube2g2 (Figure 1B) yielded slow-exchange NMR spectra and

indicated a Kd << 1 mM, consistent with the ITC data. An unex-

pectedly large number of the Ube2g2 HN-N peaks shifted in

the presence of G2BR, requiring reassignment. The 13C-edited

HSQC spectra of the methyl resonances of Ile, Leu, and Val resi-

dues (data not shown) indicated a localized binding site, which

correlates with the largest shifts observed in Figure 1B. The

Molecular Cell 34, 674–685, June 26, 2009 ª2009 Elsevier Inc. 675

Molecular Cell


Table 1. Dissociation Constants of E2-E3 Interactions

Complex Kd DH (kJ mol�1) DS (J K�1 mol�1T�1) Method NMR Exchange Timescale

Ube2g2:G2BR 21 (± 4) nM �56.3 (± 0.01) �41.8 (± 0.04) ITC slow

Ube2g2:G2BRDN 740 (± 110) nM �9.80 (± 0.40) 83.6 (± 1.43) ITC slow

Ube2g2:G2BRDC 192 (± 22) mM n.d.a n.d. NMR fast

Ube2g2:G2BRM4-1 55 (± 18) mM n.d. n.d. NMR fast

Ube2g2:G2BRM4-2 9.5 (± 4) mM n.d. n.d. NMR fast

Ube2g2:gp78-RING 144 (± 10) mM n.d. n.d. NMR fast

(Ube2g2:G2BRDN):gp78-RING 29 (± 5) mM n.d. n.d. NMR fast

(Ube2g2:G2BR):gp78-RING 3 (± 1) mM n.d. n.d. NMR fasta n.d. = not determined.

secondary structure based on chemical shifts of Ube2g2:G2BR

was identical to free Ube2g2, and NOESY spectra of

Ube2g2:G2BR exhibited equivalent patterns of connectivities

between HN-HN, HN-methyl, and methyl-methyl protons

compared to free Ube2g2, implying that the overall structure of

Ube2g2 did not change significantly.

The binding surface was determined by chemical shift

mapping on Ube2g2 and by intermolecular NOESY experiments.

Chemical shift mapping for Ube2g2 indicates the primary binding

site is on b strands b1–b3 (Figure S2). In addition, the C-terminal

regions of helices a1 and a4 are perturbed by G2BR binding.

Intermolecular NOESY cross-peaks were observed between

G2BR and the methyl and amide protons of Ube2g2 (Figure S3)

that correspond to the surface indicated in blue on unbound

Ube2g2 in Figure 1C. These NOEs refined the contact surface

to residues V25, A26, E31, E38, L40–M42, E45, E50, F51–V53,

V159, L163, and L165. This surface includes the hydrophobic

patch formed by V25, A26, L40–M42, and F51–V53 that is mostly

conserved in other E2s (Hamilton et al., 2001; Moraes et al., 2001;

Brzovic et al., 2006). The G2BR-binding site also includes nega-

tively charged residues flanking the hydrophobic core. From the

perspective of the G2BR, 15N-HSQC spectra (Figure 1D) of

a biosynthetically prepared G2BR exhibited poor chemical shift

dispersion, consistent with a random coil conformation. The

backbone chemical shifts were assigned in the free G2BR

peptide, and, except for indications of a nascent 4 residue helical

turn at V583–K586, the peptide lacks any regular secondary

structure. The spectrum of G2BR in the presence of Ube2g2

exhibits a dramatic increase in spectral dispersion and reso-

nance linewidths consistent with a 1:1 complex of Ube2g2:G2BR

(Figure 1D). This suggests that the G2BR must fold into a compact

regular secondary structure utilizing all 27 residues to fit on the

defined E2-binding site. Based on this, we redefine the G2BR

as amino acids 574–600 of gp78 instead of 579–600 as originally

defined (Chen et al., 2006).

The Ube2g2:G2BR Crystal Structure Reveals DistantChanges that Impact E2 Loading of UbiquitinThe Ube2g2:G2BR complex was crystallized, forming rod-

shaped crystals (0.1 mm 3 0.3 mm 3 0.1 mm). These diffracted

to 1.8 A resolution (Table 2). The structure shows that the

Ube2g2 backbone is largely unchanged in the presence of

G2BR (Figure 2A), as predicted by NMR measurements. The


conserved secondary structural elements include a1 = T4–L18,

b1 = G23–P28, b2 = E36–M42, b3 = V53–S59, b4 = K70–F73,

310 helix = S91–L93, a2 = V116–A128, a3 = V138–D146, and

a4 = R148–L163. Strands b1–b4 form an antiparallel b sheet

(Figures 2A and 2B). A dynamic region in the b4a2 loop is present

between residues H94 and W110. This corresponds to an acidic

extension (aa 96–108) that, in mammals, is limited to Ube2g2 and

two other E2s (Ube2g1 and Ube2r1 [Cdc34 in yeast]). The back-

bone root-mean-square deviation (rmsd) between the free and

bound Ube2g2 is 1.8 A over all residues and decreases to 0.9 A

if residues 96–108 in the b4a2 loop are excluded.

Key structuralchanges wereobserved inUbe2g2near the active

site upon binding the G2BR. Access to the active site Cys (C89) is

via a channel flanked on either side by b4a2 loop and the a2a3 loop

(Figure 2A). The b4a2 loop was observed to exhibit dynamic

behavior for aa 96–108 in the crystal structure of free Ube2g2

(Arai et al., 2006). In fact, there were three molecules in the asym-

metric unit, and the major difference between the molecules was

the conformation of the b4a2 and a2a3 loops (Figure 3A). These

conformations are ordered; however, they exhibit higher B factors

than the rest of the structure (Figure S2). The dynamic region of the

b4a2 loop contains a short 310 helix and generally extends away

from the protein in the three conformations in the free form;

however, in the Ube2g2:G2BR complex presented here, the 310

helix is gone, and a region of the loop (P100–Y103) orients back

toward C89. The multiple conformations of these loops, which

appear to shift to a new average state in the Ube2g2:G2BR

complex,and thehighB factors in the crystal structuresareconsis-

tentwithdynamicaveraging assuggested bychemical shift effects

observed in solution (Figure S2). The present structure may repre-

senta low-energypopulation of the average, inwhich the proximity

of Y103 and C89 changes from 20.8 A in unbound Ube2g2 to 3.8 A

in the complex. Inaddition, the a2a3 loop (comprising N131–G135)

approachesC89 in the complex.This inwardconformation isstabi-

lized in the 1.8 A crystal structure by a new network of water-medi-

ated hydrogen bonding, including Y103, C89, and Y83, as well as

a network including E133 and S91. The structural modifications of

these two loops decrease accessibility around the active site

(compare Figure 1C to 4B and Figure 3B to 3C). These changes

are accompanied by an altered orientation of the C89 side chain

from pointing toward the b4a2 loop in the unbound formtopointing

away from the loop (�80% probability) with bound G2BR

(Figure 2A and compare Figure 3B to 3C).

Molecular Cell


The multiple states surrounding the active site seen in the

crystal structures and the shift in conformational averaging in

the Ube2g2:G2BR complex in solution suggest that these

changes may have an impact on interactions with E1 or ubiquitin

bound to C89. To further evaluate this, we compared the struc-

tures of Ube2g2 and Ube2g2:G2BR with two reported E2-Ub

structures (Hamilton et al., 2001; Eddins et al., 2006). Superpo-

sition of free Ube2g2 with the E2 component of Ubc1-Ub, which

forms K48 ubiquitin chains (Chen and Pickart, 1990), and

Ubc13-MMs2-Ub, which forms K63 chains (Deng et al., 2000)

(Figure 3B), reveals that the C termini of either of the two bound

ubiquitins can readily be accommodated in the channel sur-

rounding C89. However, superposition of Ube2g2:G2BR with

the same two structures (Figure 3C) indicates that the area

around the active site becomes occluded due to rearrange-

ments of residues M101–Y103 and E133–G135 (within the

b4a2 loop and a2a3 loop, respectively), resulting in steric

clashes with the C termini of the two ubiquitins. In Figure 3C,

Table 2. Data Collection and Refinement Statistics

Data Collection

Space group P212121

Cell dimensions

a, b, c (A) 48.92, 60.15, 61.64

a, b, g (�) 90, 90, 90

Resolution (A) 50–1.8 (1.86–1.8)a

Number of observations 105668 (5851)

Number of unique reflections 16657 (1272)bRmerge 7.8 (43.7)

I/s 22.4 (2.7)

Completeness (%) 95.4 (74.2)

Redundancy 6.4 (4.6)

Refinement

Resolution (A) 43–1.8 (1.86–1.8)cRworking (%) 19.3 (23.1)dRfree (%) 24.1 (27.4)

Number of atoms/B factors (A2)

Protein 1318/33.1

Peptide 260/34.4

Water 164/40.7

Rmsd

Bond lengths (A) 0.005

Bond angles (�) 0.92

Ramachandran plot

Most favored region (%) 87.7

Additional allowed region (%) 12.3

Generously allowed region (%) 0

Disallowed region (%) 0a Values in parentheses are for the highest resolution cell.b Rmerge = Sj(I�<I>)j/s(I), wherein I is the observed intensity.c R factor = ShkljjFoj � jFcjj / ShkljFoj, calculated from working data set.d Rfree is calculated from 5% of data randomly chosen and not included in

refinement.

Y103 is buried and is not visible. These structure-based models

predict direct consequences for loading of G2BR-bound

Ube2g2 with ubiquitin from E1. This was tested by comparing

ubiquitin loading of Ube2g2 in the presence of either a control

scrambled peptide (Scr) (Figure 1A) or the G2BR. The G2BR

resulted in a marked decrease in the rate of E2 loading at

30�C (Figure 3D) and almost no detectable loading at 12�C

(Figure S4). Deletion of the extended acidic portion of the

b4a2 loop (aa 96–108; Ube2g2D96–108), which is the major

contributor to steric crowding around the active site, decreased

the G2BR effect by almost 75%, and G2BR binding was retained

(Figures 3D and S5).

Ube2g2-Bound G2BR Forms an a Helix with ExtensiveContacts across the Backside of the E2The crystal structure of Ube2g2:G2BR demonstrates that the

G2BR assumes a completely a-helical fold in the 1:1 complex

and binds to a surface comprising the b sheet (b1–b3) and the

C termini of a1 and a4 (Figure 2A), which is consistent with the

solution NMR data (Figure 1C). The buried surface at the inter-

face of Ube2g2 and G2BR is �1950 A2. The entire peptide is

well ordered, and there is an extensive network of contacts

between the G2BR and Ube2g2, comprising both hydrophobic

and ionic or hydrogen-bonding contacts (Figures 2C, 2D, and

2E and Table S1). The contact network is consistent with the

thermodynamic data for formation of this complex and suggests

that the recognition is highly specific. In the G2BR a helix, there is

evidence for 24 hydrogen bonds between all i and i+4 pairs,

beginning with the Ser 574 carbonyl oxygen to Arg 578 NH and

running through Arg 596 carbonyl oxygen to Lys 600 NH. As

amino acids 574–600 extend completely across the backside

of Ube2g2, this suggests that extensions beyond this region

do not interact with Ube2g2. This is in agreement with previous

data (Chen et al., 2006) and NMR studies of aa 574–643 of

gp78 (unpublished data).

The presence of extensive contacts between Ube2g2 and

G2BR suggests that single-point mutations will not disrupt

binding or activity. The initial characterization of the G2BR

(Chen et al., 2006) indicated that the N- and C-terminal ends of

the G2BR were each critical both for binding Ube2g2 and for

the cellular function of gp78. To examine this observation, we as-

sessed binding of G2BRDN and G2BRDC (Figure 1A) to Ube2g2.

G2BRDC binds Ube2g2 with relatively weak affinity (Kd = 192

[± 22] mM) (Table 1). The affinity between G2BRDN and Ube2g2

is significantly stronger (Kd = 740 [± 110] nM) but nonetheless

exhibits an �35-fold decrease in affinity compared to wild-type

G2BR. This confirms that the N- and C-terminal regions of

G2BR both contribute directly to the high-affinity binding

observed with the intact domain. Binding of either G2BRDN or

G2BRDC to Ube2g2 causes a subset of the observed chemical

shift changes seen with the G2BR, consistent with their pre-

dicted contacts (data not shown).

On the basis of the Ube2g2:G2BR structure, we designed two

peptides with four mutations each to assess the most important

interactions, G2BRM4-1 and G2BRM4-2 (Figure 1A). These

peptides were 15N labeled and examined by NMR (Figure S6).

The 15N-HSQC spectra of both peptides indicated random coil

conformations characteristic of wild-type G2BR. Titration of


Molecular Cell


G2BRM4-1 and G2BRM4-2 with unlabeled Ube2g2 yielded Kds of

55 (± 18) mM and 9.5 (± 4) mM, respectively (Table 1). These

findings, combined with the data for G2BRDN and G2BRDC,

underscore the highly distributed nature of the contacts in

Ube2g2:G2BR binding.

The G2BR Enhances the Affinity of Ube2g2for the gp78 RING FingerThe positioning of the Ube2g2:G2BR interface on the backside

of Ube2g2 suggests that this interaction should not present

a direct steric impediment to the interaction of Ube2g2 with

Figure 2. Crystal Structure of the

Ube2g2:G2BR Complex

(A) Ribbon representation of the superimposed

Ube2g2:G2BR complex with free Ube2g2 (PDB

entry 2CYX). G2BR is cyan, and Ube2g2 is light

green in the complex. Free Ube2g2 is shown in

orange.

(B) Linear representation of the secondary struc-

ture and binding regions of Ube2g2. a helices are

represented by open rectangles; b strands, by

filled arrows; and the active site Cys, by a red

dot. Binding regions are indicated below the

sequence line as RING finger (magenta) and

G2BR (green). The position of Ube2g2’s extended

dynamic loop is indicated in orange.

(C) Hydrophobic side chains of G2BR (light blue,

residues in black) lock into the hydrophobic

surface of Ube2g2 (dark green, residues in yellow).

(D) Intermolecular hydrogen bonds and salt

bridges between G2BR and Ube2g2 are shown.

Side chains of G2BR are shown in blue; residues,

in black; the Ube2g2 contact side chains and resi-

dues, in red. The P21 and I24 side chains of

Ubeg2g2 were not displayed because the interac-

tion is through backbone hydrogen bonds.

(E) Contacts between Ube2g2 (green) and G2BR

(blue) indicating residues involved in hydrogen

bonds, salt bridges, and hydrophobic interactions.

Black lines link each residue to its reciprocal

contact, and X denotes G2BR residues that do

not have direct contacts in the interface.

the gp78 RING finger-binding site (Zheng

et al., 2000; Brzovic et al., 2003; Domi-

nguez et al., 2004) (Figure 2A). To eval-

uate possible allosteric effects of G2BR

on RING finger binding, the interaction

of isotopically labeled Ube2g2 with

gp78 RING finger was monitored by

NMR (Figure 4). The gp78 RING finger-

binding interface on Ube2g2 consists of

the N-terminal end of a1, the b3b4 loop

(F62–P69), and part of the b4a2 loop

(W110–S115) (see Figures 2A and 2B

for secondary structure elements). The

solution structure of the gp78 RING

finger is similar to other RING finger

structures (R.D. and R.A.B., unpublished

data), and a reverse labeling experiment using isotopically

labeled gp78 RING finger confirmed that the gp78 RING finger

side of the binding surface is similar to other RING finger:E2

interactions. The interaction exhibited fast exchange

(Figure 4A) and a Kd of 144 (± 10) mM (Table 1 and Figure S7).

This is consistent with the low affinity of many RING finger:E2

interactions (Lorick et al., 2005; Christensen et al., 2007). The

affinity of the gp78 RING finger for the Ube2g2:G2BR complex

was also determined. While the binding interface was

unchanged and remained in fast exchange, strikingly, the Kd

decreased by �48-fold to 3 (± 1) mM (Table 1 and Figure S7).


Molecular Cell


Separate binding experiments confirmed that the G2BR and

RING finger do not directly interact in the gp78 RING finger:

Ube2g2:G2BR complex (data not shown). The allosteric rela-

tionship of Ube2g2:gp78 RING finger affinity to Ube2g2:G2BR

association was tested by measuring the affinity of gp78 RING

finger for Ube2g2 in the presence of G2BRDN, which exhibits

an affinity for Ube2g2 intermediate between the full G2BR and

G2BRDC. The measured Kd was 29 (± 5) mM (Table 1), which

indicates that even a smaller fragment of G2BR has effects

that translate through Ube2g2 and increase its affinity for the

gp78 RING finger.

Figure 3. G2BR-Induced Structural Changes

in Ube2g2 Occlude the Area around the

Active Site and Correlate with Ubiquitin

Loading

(A) Superposition of active site region (full struc-

tures shown in small inset) for four Ube2g2 mole-

cules (yellow, cyan, and magenta from the ligand-

free Ube2g2 in PDB entry 2CYX and green in

Ube2g2:G2BR) showing the conformational flexi-

bility of the b4a2 loop.

(B and C) Images showing the surface rendering of

Ube2g2 and Ube2g2:G2BR combined with the

potential orientation of ubiquitin chains, based on

known E2-Ub structures. Ube2g2 was superim-

posed onto the E2 coordinates of two published

E2-Ub structures: Ubc1-Ub (PDB entry 1FTX,

rmsd = 1.8A) and Ubc13-MMs2-Ub (PDB entry

2GMI, rmsd = 1.4A). We display only the surface

of Ube2g2 and the C-terminal end of the ubiquitin

molecule (in ball and stick form) for Ubc1-Ub

(blue) and Ubc13-MMs2-Ub (magenta). In (B), the

free Ube2g2 structure is rotated relative to the

orientation of Figure 1C by 180� about the vertical

axis and zoomed in on the active site. The active

site Cys (C89) backbone is yellow, and its side

chain is red. Some residues of Ube2g2 that play

a role in the allosteric change are labeled in green.

R74 of both ubiquitin tails are indicated; the

C-terminal diglycine approaches C89. In (C), the

G2BR-bound form of Ube2g2 is shown in an iden-

tical orientation as in (B).

(D) 35S-labeled Ube2g2 or Ube2g2D96–108 gener-

ated by in vitro translation in E. coli lysate was incu-

bated with 100 nM E1 and ubiquitin-lacking lysines

(Ub K0), so as to avoid formation of polyubiquitin

chains. The formation of thiolester-linked Ube2g2

(E2�Ub) was assessed at 30�C with saturating

(4 mM) G2BR peptide or a control ‘‘scrambled’’

peptide (Scr). Shown is the average of two experi-

ments for each condition. Rate constant, K, and

95% confidence index are shown for each condi-

tion.

G2BR Enhances RINGFinger-Dependent Ubiquitylationby Ube2g2gp78 is a substrate for its own ubiquityla-

tion in cells (Fang et al., 2001; Chen et al.,

2006). To begin to assess the effect of the

G2BR on ubiquitylation, we employed

a GST fusion of the cytoplasmic domain of gp78 (GST-gp78C)

in an autoubiquitylation assay (Lorick et al., 1999). Ube2g2 was

provided in�5-fold molar excess relative to glutathione Sephar-

ose-immobilized GST-gp78C, and ubiquitylation of bead-bound

material was assessed. Ubiquitylation was totally dependent on

an intact gp78 RING finger (Figure 5A), and mutations of two

key residues in the G2BR (L582S/L589S; gp78CL582,589S) signif-

icantly decreased ubiquitylation. A truncated form of GST-gp78C

lacking the G2BR (GST-gp78CD577–643) also demonstrated

markedly diminished ubiquitylation (Figure 5B), consistent with

G2BR-dependent increased affinity of Ube2g2 for the gp78


Molecular Cell


RING finger. However, when G2BR peptide was provided in

trans, there was a marked increase in ubiquitylation of truncated

gp78 (Figure 5B). This rescue of activity was not observed with

the G2BRDN, G2BRDC, G2BRM4-1, or G2BRM4-2 peptides (Figures

5C and 5D). To determine whether the G2BR peptide also

enhances ubiquitylation of heterologous proteins, we took

advantage of gp78’s function as an E4 in ubiquitylating proteins

already modified with a single ubiquitin (Morito et al., 2008). A

fusion protein of ubiquitin and GFP with a C-terminal His6 tag

(Ub-GFP-His6) was ubiquitylated by GST-gp78CD577–643

as assessed using Flag-tagged ubiquitin (Figure 5E). As with

gp78 autoubiquitylation, ubiquitylation of Ub-GFP-His6 by GST-

gp78CD577–643 was substantially increased in the presence of

G2BR. Thus, the effect of the G2BR applies to ubiquitylation of

a heterologous substrate, as well as to autoubiquitylation.

To evaluate the effect of G2BR on substrate ubiquitylation

using the full-length gp78 cytoplasmic tail, gp78C and

gp78CL582,589S were compared. gp78C resulted in easily detect-

able, high-molecular weight ubiquitylated Ub-GFP-His6, which

was not evident with gp78CL582,589S (Figure 5F). As

gp78CL582,589S showed some persistent autoubiquitylation in

Figure 5A, these reactions were carried out by combining

G2BR mutants with double mutations of Ube2g2 in key contact

points (Figure 5G; see Figure 2 and Table 1 for Ube2g2:G2BR

contacts). Though none of the double mutants of Ube2g2

substantially decreased ubiquitylation with either gp78C or

a single mutation (gp78CL582S), combining any of these E2

mutants with gp78CL582,589S resulted in a complete loss of ubiq-

uitylation. Collectively, these findings demonstrate the functional

importance of structurally defined key contact residues in the

Ube2g2-G2BR interface.

G2BR Enhances Ubiquitylation by Ube2g2with Other RING FingersUbe2g2 also functions with other RING finger ERAD E3s (unpub-

lished data). Two of these, HsHRD1 and Trc8, are implicated in

human disease (Kostova et al., 2007). These E3s also function,

at least in vitro, with members of the UbcH5 (Ube2d1–3) E2

family (Lorick et al., 1999; Nadav et al., 2003; Kikkert et al.,

2004). HsHRD1 and Trc8 lack identifiable regions that are anal-

ogous to the G2BR. Therefore, we asked whether the enhanced

ubiquitylation observed with the G2BR was unique to the gp78

RING finger. Addition of the G2BR to ubiquitylation reactions

utilizing GST fusions of the C-terminal RING finger-containing

regions of either HsHRD1 or Trc8 resulted in a marked increase

in RING finger-dependent autoubiquitylation (Figure 5H, top,

lanes 5 and 8, and Figure S8). Ubiquitylation mediated by these

E3s, as well as by GST-gp78CD577–643, was not increased by the

G2BR when UbcH5B was used as the E2 (Figure 5H, bottom).

Similarly, critical mutations in the G2BR do not decrease ubiqui-

tylation by UbcH5B (Figure S9). Thus, changes in the ERAD E2,

Ube2g2, induced by binding of the G2BR at a site distant from

where this E2 interacts with RING fingers, enhances ubiquityla-

tion with at least three different mammalian E3s. This indicates

both the specificity of the G2BR for Ube2g2 and its apparent

effect on increasing productive interactions between Ube2g2

and RING fingers.

Increased Affinity of Ube2g2 for the gp78 RING FingerAccounts for the Enhanced UbiquitylationTo further evaluate the effect of the G2BR, we assessed the rate

of discharge of ubiquitin from Ube2g2, based on a previously

used approach (Petroski and Deshaies, 2005), in the presence

of saturating amounts of G2BR or an equal concentration of

Scr. In these reactions, acceptors for ubiquitin are other proteins

in the reaction mix, including bacterial proteins and free ubiquitin

added in excess. In the absence of the RING finger, discharge of

ubiquitin from Ube2g2�Ub was slow and unaffected by G2BR

peptide (Figure 5I). In the presence of 8 mM gp78 RING finger,

loss of Ub-bound Ube2g2 was markedly accelerated. This was

significantly increased by saturating amounts of G2BR

(Figure 5I). We wished to determine whether this apparent

increased rate of discharge can be accounted for by an

increased population of Ube2g2:RING finger due to the

Figure 4. Interactions between gp78 RING

Finger and Ube2g2:G2BR Complex

(A) Ube2g2:G2BR complex was titrated with gp78

RING finger followed by acquisition of 15N-HSQC

spectra of isotopically labeled Ubeg2g2 at each

titration point. 15N chemical shifts in parts per

million (ppm) are indicated on the y axis, and 1H

chemical shifts in ppm are on the x axis. Three of

the affected residues of Ube2g2 (N19, L66, and

V113) are shown. The peaks shift from the free

(blue) form toward the bound form (magenta)

with addition of gp78 RING finger. The dissocia-

tion constant was determined by fitting the peak

positions against ligand: protein concentrations.

(B) The surface representation of Ube2g2:G2BR

shows the G2BR interface (blue), RING interface

(magenta), and active site cysteine (red).


Molecular Cell


presence of G2BR (<5% Ube2g2 bound with Scr; >50% bound

with G2BR) or by as yet unknown allosteric effects on the

Ube2g2:gp78 RING finger complex mediated by the G2BR.

Therefore, experiments were carried out with concentrations of

gp78 RING finger at which approximately equal amounts of

RING finger are bound to Ube2g2. Under these conditions, no

significant increase in discharge rate was observed in the pres-

ence of G2BR (Figure 5J). Thus, the G2BR-mediated increase

in affinity of Ube2g2 for the RING finger provides a molecular

basis for the accelerated discharge of ubiquitin from

Ube2g2�Ub and, by extension, for the observed enhancement

of ubiquitylation.

DISCUSSION

Structural Basis for the High-Affinity G2BR Bindingto Ube2g2The NMR and X-ray crystallographic determination of the G2BR-

binding site on Ube2g2 provides an explanation for its high-

affinity interaction with gp78. The G2BR binds Ube2g2 through

an extended region of the core UBC domain of Ube2g2 that

includes the C-terminal ends of both the a1 and a4 helices and

extensive contacts with the intervening b sheets (b1–3). This

backside binding substantially overlaps the noncovalent binding

site for ubiquitin on UbcH5C (Brzovic et al., 2006). Whereas ubiq-

uitin binds UbcH5C with a Kd of �300 mM, which is similar to the

analogous binding of ubiquitin to Ube2g2 (R.D. and R.A.B.,

unpublished data), the binding of the G2BR to Ube2g2 is of

higher affinity by > 10,000-fold. The basis for this difference is

explained by the interacting interfaces. Ubiquitin, characterized

by a stable, ordered structure, interacts with E2s through its

hydrophobic face centered on I44. The G2BR, on the other

hand, folds from an unstructured state into a well-ordered a helix

upon interacting with Ube2g2. At their interface, hydrophobic

side chains along the spine of the G2BR a helix interlock with

Ube2g2 in a fashion similar to the UbcH5C:Ub complex. Addi-

tionally, charged and polar residues distributed along the

G2BR a helix on either side of the hydrophobic spine (Figures

2C and 2D) form salt bridges and hydrogen bonds with

Ube2g2, resulting in a high-affinity complex with a Kd of�21 nM.

Implications of Ube2g2:G2BR for Ubiquitylationand ERADUntil now, the existence of the G2BR as a high-affinity binding

site for Ube2g2 had been assumed to primarily provide a means

to increase the level of Ube2g2�Ub in proximity to gp78 and to

enhance ubiquitylation (Chen et al., 2006). We have now uncov-

ered additional effects of the G2BR. This highly specific 27 aa

binding site for Ube2g2 has the striking effect of increasing the

affinity of Ube2g2 for the gp78 RING finger as a consequence

of conformational/allosteric changes in Ube2g2. The basis for

the dramatic change in Kd, from 144 mM to 3 mM, is not yet fully

understood and awaits further structural studies. A striking

consequence of this increased affinity is the increased associa-

tion of Ube2g2 with the gp78 RING finger, thereby facilitating the

discharge of ubiquitin from Ube2g2�Ub through as yet unde-

fined RING finger-mediated effects (Ozkan et al., 2005; Petroski

and Deshaies, 2005). This is reflected in enhanced ubiquitylation,

even when the G2BR peptide is provided in trans to Ube2g2

together with the cytoplasmic domain of gp78 lacking the

G2BR sequence. Significantly, at least in vitro, the G2BR also

increases ubiquitylation by heterologous ERAD RING finger

E3s. In the cell, this potential for cross-talk between different

ERAD ubiquitin ligases has the potential to contribute to associ-

ations between ERAD RING finger E3s and, more importantly,

to promote synergistic interactions among these proteins

(Ye et al., 2005; Morito et al., 2008). Similarly, if the reported

gp78-oligomerization-dependent formation of K48 ubiquitin

chains on C89 of Ube2g2 occurs in cells (Li et al., 2009), this

will be facilitated by the enhanced affinity of Ube2g2 for the

gp78 RING finger with G2BRs. This domain can serve both as

platforms for Ube2g2 bearing nascent ubiquitin chains and as

a means to enhance transfer of ubiquitin from heterologous

Ube2g2s.

In addition to the increase in RING finger binding, the

Ube2g2:G2BR structure, compared to apo-Ube2g2, reveals

a conformation in which there is narrowing of the channel projec-

ting from the active site Cys89. This is largely due to reposition-

ing of the extended mobile acidic portion of the b4a2 loop,

including a dramatic alteration in orientation of side chains of

M101 and Y103. All of the available structural data indicate

that this region is dynamically disordered (Arai et al., 2006; Li

et al., 2009; this study). One consequence of this repositioning

is a substantial delay in formation of Ube2g2�Ub in the presence

of G2BR. Depending on the rate limiting step(s) in vivo, slowing of

E2 loading with ubiquitin in the presence of the G2BR could allow

for ‘‘proofreading’’ by deubiquitylating enzymes in either sub-

strate selection or chain linkage. The region analogous to the

b4a2 loop is important for interactions between other E2-E3

pairs (Lorick et al., 2005), as well as for Ube2g2:gp78 RING finger

(this study). The acidic extension in this loop is also found in

Cdc34. Mutations in acidic residues in this region in both

Ube2g2 and Cdc34 translate into decreased RING finger-depen-

dent formation of K48-linked polyubiquitin chains (Li et al., 2007;

Petroski and Deshaies, 2005). Moreover, Cdc34-Ub recently has

been shown to manifest �2-fold lower Kd for the core SCF E3

than for Cdc34 (Saha and Deshaies, 2008). As the net effect of

the G2BR, either in cells or in vitro, is to enhance ubiquitylation,

potential effects of this dynamic loop on modulating transfer of

ubiquitin from Ube2g2�Ub, formation of K48 ubiquitin chains,

or in differential RING finger binding of Ube2g2�Ub versus

Ube2g2 may be of equal or greater significance than the

pronounced inhibition of loading with ubiquitin that we observe.

Addressing these possibilities and the unresolved question of

whether ubiquitin can be transferred from E1 to Ube2g2 bound

either to the full cytoplasmic tail of gp78 or the isolated G2BR

are important questions in ERAD and in E2 function that will

require additional in vitro and cellular approaches.

Existence and Implications of E2-Binding Sites Distinctfrom Ligase DomainsE2s interact with E1, as well as with HECT, RING, and RING

finger-like domains on E3s. The question now arises as to the

prevalence of other functionally significant E2 interactions. A

well-characterized example is the E2-like molecule Mms2

(UEV1a), which binds Ubc13 through a region distinct from the


Molecular Cell



Molecular Cell


G2BR-Ube2g2 interface and facilitates formation of K63-linked

ubiquitin chains (Eddins et al., 2006). Another example,

mentioned above, is ubiquitin, which plays a role in the proces-

sivity of BRCA1-mediated ubiquitin chain formation, presumably

through alignment of multiple UbcH5C�Ub complexes (Brzovic

et al., 2006; Christensen et al., 2007). The high-affinity interaction

of Ube2g2:G2BR precludes backside ubiquitin binding in the

context of Ube2g2 bound to gp78. However, it does not exclude

that alignment of multiple E2�Ub complexes (not necessarily

Ube2g2) in vivo could occur in the context of a G2BR-bound

Ube2g2�Ub and play a role in chain formation.

There are several examples in which regions of E3s, which are

not included in their canonical ligase domains, bind E2s, e.g.,

Nedd4 and Ubr1p. For these, neither the sites of interaction on

their respective E2s nor the functional effects of this binding

are known (Madura et al., 1993; Hatakeyama et al., 1997). There

is evidence that SCF E3s recruit Cdc34 through part of the

C-terminal extension of this E2 (Wu et al., 2002). Yeast Ubc7p,

which is the ortholog of Ube2g2, is recruited by Cue1p to the

ER membrane to function with the ERAD E3s Hrd1p and

Doa10p (Kostova et al., 2007). Recent findings suggest that

the 180 amino acid cytoplasmic domain of Cue1p activates

Ubc7p in vitro in a RING finger-independent manner through

unknown mechanisms (Bazirgan and Hampton, 2008; Kostova

et al., 2009). Moreover, an �50 aa domain in Cue1p, with

some sequence homology to G2BR, directly binds Ubc7p. This

domain is sufficient to activate ERAD by Hrd1p in vivo and stim-

ulates ubiquitylation in vitro, analogous to the G2BR (Kostova

et al., 2009), and thus may represent a yeast equivalent of the

G2BR.

A possible parallel to gp78 and Ube2g2 comes from the

SUMO E3 Nup358/RanBP2. This E3 binds the SUMO E2

(Ubc9) through regions on Ubc9 analogous to interactions

between ubiquitin E3s and E2s. However, this E3 also con-

tacts Ubc9 through a second region with similarity to the

Ube2g2:G2BR interface (Reverter and Lima, 2005). As pointed

out by Reverter and Lima, mutations in this interface impact

Ubc9 binding and Nup358/RanBP2 function (Pichler et al.,

2004; Tatham et al., 2005). It will be of interest to know whether

this second site of E2:E3 interaction has analogous effects to

those observed in this study.

It seems reasonable to postulate that E2-binding sites within

E3 complexes but distinct from canonical ligase domains may

be a property of a substantial fraction of E3s. To what extent

these result in functionally significant allosteric effects on E2s,

as demonstrated herein, now becomes an exciting area for

future research.

EXPERIMENTAL PROCEDURES

NMR Spectroscopy

NMR samples were prepared in 50 mM Tris, 2 mM TCEP (pH 7.5) buffer, and

experiments were performed at 25�C. NMR spectra were acquired on 600 and

800 MHz Varian INOVA spectrometers equipped with triple-resonance

gradient cryoprobes. Details of resonance assignments, binding titrations,

and intermolecular NOESY experiments are provided in the Supplemental

Experimental Procedures available online.

X-Ray Diffraction

Crystallization screens were carried out with a Phoenix robot (Art Robbins

Instruments). The crystals were flash-frozen in liquid N2 after a short soak in

a cryoprotection solution. A native data set was collected at beamline 22-ID

of the Advanced Photon Source, Chicago. The structure was solved by molec-

ular replacement. The initial Fo – Fc map revealed the electron density for the

G2BR. Details of crystallization, data acquisition, structure solution, model

building, and structure refinement are provided in Supplemental Experimental

Procedures.

Isothermal Titration Calorimetry

ITC was carried out using a VP-ITC microcalorimeter (MicroCal LLC, North-

ampton, MA) at 25�C. The typical experiment included injection of 25–27

aliquots (10 ml each) of 0.1–0.5 mM peptide solution into a 0.01–0.10 mM

protein solution in the ITC cell (volume �1.4 ml), stirring at 300 rpm. Additional

details are provided in Supplemental Experimental Procedures.

In Vitro Ubiquitylation, E2 Loading, and Discharge

Autoubiquitylation was carried out as described (Kostova et al., 2009; Lorick

et al., 1999). Ubiquitylation of bacterially expressed purified Ub-GFP-His6

Figure 5. G2BR-Mediated Increase in Ube2g2:gp78 RING Finger Affinity Results in Enhanced Ubiquitylation

(A) Glutathione Sepharose-bound GST fusions of the entire gp78 cytoplasmic tail (aa 309–643; GST-gp78C), an inactivating mutation in the RING finger

(GST-gp78CRM) or in the G2BR (GST-gp78CL582,589S), or GST alone were incubated for 90 min in the presence of Ube2g2 and E1. After washing, ubiquitylated

bead-bound material was assessed by SDS-PAGE and immunoblotting with antiubiquitin. See Figure S10 for Coomassie blue stain of fusion proteins.

(B) Glutathione Sepharose-bound GST-gp78C, a truncation at amino acid 577 at the beginning of the G2BR (GST-gp78CD577–643), or GST alone was incubated

with or without G2BR peptide as indicated and assessed in (A).

(C and D) (C) and (D) were carried out as in (A) using GST-gp78CD577–643 and the indicated synthetic or recombinant peptides. Recombinant wild-type G2BR

peptide is indicated by an asterisk to distinguish from the synthetic wild-type peptide.

(E) Ubiquitylation of Ub-GFP-His6 was carried out under the indicated conditions. The asterisk denotes two control samples in which Ub-GFP-His6 was added

after the reaction was first terminated by the addition of 10% SDS for 10 min followed by 8 M urea. Following addition of urea, Ub-GFP-His6 was purified on Ni+

Sepharose beads, and samples were resolved by SDS-PAGE.

(F) Ubiquitylation of Ub-GFP-His6 was carried out as in (E) for 60 min.

(G) Ubiquitylation reactions were carried out with GST-gp78C or the indicated Leu to Ser mutations together with wild-type Ube2g2 or the indicated double muta-

tions of Ube2g2.

(H) GST fusions of the cytoplasmic tails of HsHRD1, Trc8, or truncated gp78 were incubated as in (A) with the indicated peptides and E2s.

(I) 35S-labeled Ube2g2 generated as in Figure 3D was loaded with wild-type ubiquitin for 10 min followed by inactivation of E1 by NEM (5 mM). Discharge of ubiq-

uitin from Ube2g2 (<100 nM), in the presence of either G2BR or Scr (4 mM) with or without gp78 RING finger (8 mM), was monitored by measuring the fraction of

Ube2g2�Ub remaining at each time point. Shown on the left is a representative experiment using gp78 RING finger. Plotted on the right is the average of three

independent experiments; error bars represent SD.

(J) Discharge experiments as in (I) were carried out for 2 or 5 min at the indicated concentrations of gp78 RING finger. Shown on the left are images demonstrating

loss of ubiquitin from Ube2g2. The insert on the right summarizes data from discharge experiments from both (I) and (J). Discharge rate constants, K, are shown

for each experiment.


Molecular Cell


(�500 nM) was carried out using glutathione Sepharose 4B bound GST-

gp78CD577–643. Reactions were terminated by 2% SDS (final). After 10 min,

samples were diluted with 8 M urea in 50 mM Tris (pH 7.4) to 0.1% SDS. Ub-

GFP-His6 was isolated on Ni2+ beads and eluted with SDS-PAGE sample buffer

after washing. 35S-labeled Ube2g2 was translated in the S30 T7 bacterial TnT

system (Promega) and used at < 100 nM. In loading experiments, Ub K0

was used. For discharge of ubiquitin from E2, E2 was loaded with wild-type

ubiquitin for 10 min. Reactions were quenched with 5 mM NEM, and the buffer

was exchanged to 50 mM Tris (pH 7.4) with Ub (80 mM) and peptide (4 mM) with

or without purified gp78 RING finger (aa 313–393); discharge was monitored at

25�C. Additional details are provided in Supplemental Experimental Proce-

dures.

ACCESSION NUMBERS

Coordinates and structure factors of the Ube2g2:G2BR complex were depos-

ited in the Protein Data Bank under accession code 3H8K.

SUPPLEMENTAL DATA

Supplemental Data include Supplemental Experimental Procedures, 10 fig-

ures, and 1 table and can be found with this article online at http://www.cell.

com/molecular-cell/supplemental/S1097-2765(09)00341-4.

ACKNOWLEDGMENTS

We thank Stanley Lipkowitz and Philip Ryan for critical reading of this manu-

script, Mei Yang and Prasenjit Bhawmik for technical assistance, Kevin Lorick

for assistance in initial studies, and Robert Gemmill, Kazuhiro Iwai, Amy Lam,

and Emmanuel Wiertz for reagents. X-ray diffraction data were collected at the

22-ID beamline of SER-CAT, Advanced Photon Source, Argonne National

Laboratory. Characterization of all proteins (CD and mass spectroscopy)

and calorimetry were performed at the Biophysics Resource in the Structural

Biophysics Laboratory. This work was supported by the National Institutes

of Health Intramural Research Program and by a grant to A.M.W. from the

Multiple Myeloma Research Foundation.

Received: November 20, 2008

Revised: March 12, 2009

Accepted: May 12, 2009

Published: June 25, 2009

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Documents

Molecular Cell Article - Linköping University · site for p97. Unique to gp78 is a high-afﬁnity binding site for its cognate E2, Ube2g2. This Ube2g2-binding region (G2BR) is required