John Mitchell

BioinformaticsChemoinformatics

Computational ChemistryTheoretical Chemistry

2

Mitchell group – BSRC & EaStCHEM School of ChemistryPurdie Building rooms 150 &152

Lazaros Mavridis Ava Sih-Yu Chen Rosanna Alderson

Neetika Nath James Mc Donagh Luna De Ferrari

Mechanism, Annotation and Classification in Enzymes.http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

MACiE Database

Enzyme Nomenclature and Classification

EC Classification

Class

Subclass

Sub-subclass

Serial number

The EC Classification

Reaction direction arbitrary

Cofactors and active site residues ignored

Doesn’t deal with structural and sequence information

However, it was never intended to do so

Deals with overall reaction, not mechanism

A New Representation of Enzyme Reactions?

Should be complementary to, but distinct from, the EC system

Should take into account:

Reaction Mechanism

Structure

Sequence

Active Site residues

Cofactors

Need a database of enzyme mechanisms

Mechanism, Annotation and Classification in Enzymes.http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

MACiE Database

EC is not Everything

• Different mechanisms can occur with exactly the same EC number.

• MACiE has six beta-lactamases, all with different mechanisms but the same overall reaction.

EC Coverage of MACiE

Representative – based on a non-homologous dataset,and chosen to represent each available EC sub-subclass.

Structures exist for: 6 EC 1.-.-.- 61 EC 1.2.-.- 204 EC 1.2.3.-1776 EC 1.2.3.4

MACiE covers: 6 EC 1.-.-.- 57 EC 1.2.-.- 183 EC 1.2.3.- 321 EC 1.2.3.4

Coverage of MACiE

Representative – based on a non-homologous dataset,and chosen to represent each available EC sub-subclass.

Repertoire of Enzyme Catalysis

G.L. Holliday et al., J. Molec. Biol., 372, 1261-1277 (2007)G.L. Holliday et al., J. Molec. Biol., 390, 560-577 (2009)

Repertoire of Enzyme Catalysis

Enzyme chemistry is largely nucleophilic

Repertoire of Enzyme Catalysis

0

50

100

150

200

250

300

350

400

450

Reaction Types

Num

ber

of

ste

ps in M

ACiE

Protontransfer

AdN2 E1 SN2 E2 Radicalreaction

Tautom. Others

Repertoire of Enzyme Catalysis

Repertoire of Enzyme Catalysis

Repertoire of Enzyme Catalysis

Repertoire of Enzyme Catalysis

We do see a few steps corresponding to well-known organic reactions; but these are the exception.

Residue Catalytic Propensities

Residue Catalytic Functions

Predicting Enzyme Function …… and Mechanism

L. De Ferrari et al. BMC Bioinformatics 2012, 13:61

24

Data sources

EnzML: Multi-label prediction of enzyme classes using InterPro signatures,L. De Ferrari et al. BMC Bioinformatics 2012, 13:61

25

Data schema

(1,108 Uniprot proteins)

26

Predicting enzyme mechanism from Sequence

M0243 pyridoxine5'-phosphatesynthase

(EC 2.6.99.2)

M0243 pyridoxine5'-phosphatesynthase

(EC 2.6.99.2)

Predicting enzyme mechanism from Structure

Moonlighting: A starting point for evolving

a new catalytic function!

Main reaction Minor side reaction

Enzyme Evolution

Investigating the apparent independent evolutionary origins of the B1 & B3 metallo- beta-lactamases at the chemical catalytic level

Numbers of Mechanisms for Folds of Different Ages

2 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 80

200

400

600

800

1000

1200

Nitrogen-Oxygen Distance Distribu-tion

DIstance/ Angstroms

Num

ber o

bser

ved

Protein-Ligand Affinity Prediction: Scoring Functions

Prediction of Off-target Activities and Side Effects• Phospholipidosis; hERG blockade; Doping in sport; Polypharmacology

ACKNOWLEDGEMENTS

Cambridge Overseas

Trust