The Chemical Nature of Enzyme Catalysis POLAR NON- POLAR Tyr*His Gly AcidicNeutralBasic Asp Glu Gln...

The Chemical Nature of Enzyme Catalysis

PO

LAR

NO

N-

PO

LAR

Tyr* His

Gly

Acidic Neutral Basic

Asp

Glu GlnCys

Asn Ser*

Thr* Lys

Arg

AlaVal

IleLeu Met

Phe TrpPro

*OH

Amino acids

• Acid-Base Catalysis• Covalent catalysis: Nucleophilic

catalysis• Metal ion catalysis• Electrostatic catalysis• Transition state binding• Proximity-Orientation effect

Enzyme Catalysis

Acid-Base Catalysis

• An acid is a "proton donor" and a base is a "proton acceptor”

• In acid catalysis and base catalysis a chemical reaction is catalyzed by an acid or a base.

HO

H

Acid-Base Catalysis

CO=

NH

HCH

NH

+

C- OOH

OH

-d

+d

HO

H

CO=

NH

HCH

CO=

NH

HCH

CO=

NH

HCH

Acid-baseCatalysis Acid

catalysis

Basecatalysis

Both

NH

+

C- OO

HO

H

Keto enol

Slow Fast Fast Very Fast

Acid-Base Catalysis

• Hydrolases: Hydrolysis of esters, peptides, phosphate

• Isomerases: Tautomesism (keto enol; amino:imino)

Side chains of Asp/Glu/ His/Cys/Tyr/Lys act as general acid/base

Covalent catalysis: Nucleophilic catalysis

Decarboxylation of acetoacetate in to acetone

Covalent catalysis: Nucleophilic catalysis

1. The enzyme forms a covalent bond to the substrate at some point during reaction

2. Lysine in the active site forms a Schiff base with the acetoacetate. (amine nucleophilically attack carboxyl group)

3. The positive charge of the Schiff base then facilitates decarboxylation (new electrophilic group withdraw electron from reaction centre)

Covalent catalysis: Nucleophilic catalysis

Covalent catalysis: Nucleophilic catalysis

N

H

H

:B

O+

H-A

N

H

CH

HOH N

H

C + OH-

Schiff base (w PLP)

N+

HCN+

H

Lys

CH3

2-O3PO

H

O-

H2CO

CH2 CO

O-

CO2

H2C

O-

CH2

H+

H2CO

CH3

acetoacetate Enolate Acetone

RNH2

OH-

N+R H

H2C CH2 CO

O-

CO2

H2C

N

CH2

H+

H2C

N+

CH3

OH-

RNH2

R HR H

Schiff base (imine)

Activity Regulation: Metal ion catalysis

Metal ion catalysis

1. Bind to substrate for proper orientation2. Mediate oxidation reduction reaction3. Metal-Electrostatic catalysis

Metal-Electrostatic catalysis1. Charge stablization (similar to or better

than Proton (pH not altered & >1charge2. Promote nucleophilic cartalysis3. Promote reaction through charge shielding

Metal ion catalysis: Charge stablization

Metal ion catalysis: nucleophilic cartalysis

OH- is a weak nucleophilic agent but in presence of Zn it becomes a good nucleophilic

Nucleophilic cartalysis: carboxypeptidase

Activity Regulation: Electrostatic catalysis

Electrostatic catalysis: serine protease

Ser195

His 57

Asp 102

H–O–CH2

O

C–O -

=

Active Ser

H–N N

C C

C

H

H

CH2

Ser195

His 57

Asp 102

- O–CH2

OC–O–H

=

N N–H

C C

C

H

H

CH2

Substrate

If enzyme just binds substrate then there will be no further reaction

Transition state Product

Enzyme not only recognizes substrate, but also induces the formation of transition state

X

Activity Regulation: transition state binding

Activity Regulation: transition state binding

Preferred binding of the transition state complexTransition state analogues are competitive inhibitors

N

CCOO-

H

H

N

C-

H

COO-

N

CH

COO-

H

L-proline

proline racemase

planar TSD-proline

H+ H+

NCOO-

H

pyrrole-2-carboxylate

N+COO-

H

D-1-pyrroline-2-carboxylate

competitive inhibitors

Activity Regulation: Proximity-Orientation effect