Download Enzyme Nomenclature and Classification

Enzyme Mechanism
Annotation and Classification
Daniel E. Almonacid, Gemma L. Holliday, Gail J. Bartlett,
Noel M. O’Boyle, Peter Murray-Rust, Janet M. Thornton
and John B. O. Mitchell
Enzyme Nomenclature and
Classification
EC Classification
Class
Subclass
Sub-subclass
Serial number
Enzyme Nomenclature and
Classification
 In 1965, the first three-dimensional structure for an
enzyme was reported.
 Advances on biochemical techniques, e.g. site directed
mutagenesis. We know the function of amino acids in
the chemical reaction mechanisms of enzymes.
R
H O H
O
R'
R'
R
N
NH
R''
O
O
R''
β-lactamases EC 3.5.2.6
There is a need to develop new classification schemes
MACiE database
Mechanism, Annotation and Classification in Enzymes.
http://www-mitchell.ch.cam.ac.uk/macie/
Repertoire of enzyme catalysis
Heterolytic
Unimolecular
Bimolecular
Intramolecular
Homolytic
Unimolecular
Bimolecular
Intramolecular
Elimination
Addition
Substitution
Electrophilic
Bimolecular
Intramolecular
Nucleophilic
Bimolecular
Intramolecular
Homolytic
Bimolecular
Intramolecular
Electrophilic
Unimolecular
Bimolecular
Intramolecular
Nucleophilic
Unimolecular
Bimolecular
Intramolecular
Homolytic
Unimolecular
Bimolecular
Intramolecular
Ingold, C. K. Cornell
University Press,
1969.
Number of steps in MACiE
Repertoire of enzyme catalysis
140
Intramolecular
120
Bimolecular
Unimolecular
Enzyme chemistry
is largely nucleophilic
100
80
60
40
20
0
Heterolytic
Elimination
Homolytic
Elimination
Electrophilic
Addition
Nucleophilic
Addition
Homolytic
Addition
Reaction Types
Electrophilic
Substitution
Nucleophilic
Substitution
Homolytic
Substitution
Repertoire of enzyme catalysis
“Other reactions” and Named organic reactions
currently supported in MACiE
______________________________________________
Aldol Condensation
Hydride Transfer
Amadori Rearrangement
Isomerisation
A-SN1
Michael Addition
A-SN2
Nucleophilic Attack
A-SNi
Pericyclic Reaction
Claisen Rearrangement
Proton Transfer
Condensation
Radical Formation
E1cb
Radical Propagation
Group Transfer
Radical Termination
Heterolysis
Redox
Homolysis
Tautomerisation
______________________________________________
Repertoire of enzyme catalysis
450
400
Number of steps in MACiE
350
300
250
200
150
100
50
0
Proton
transfers
AdN2
E1
SN2
E2
Reaction Types
Radical
reactions
Tautom.
Others
Function of catalytic residues
In MACiE catalytic residues are those:
i) directly involved in the catalytic mechanism;
ii) modifying the pKa of a residue or water molecule directly involved
in the catalytic mechanism;
iii) stabilising a transition state or intermediate;
iv) activating the substrate.
Bartlett, G. J. et al. J. Mol. Biol., 2002, 324, 105.
Porter, C. T. et al. Nucleic Acids Res., 2004, 32, D129.
Function of catalytic residues
Main-chain spectator
Side-chain spectator
Main-chain reactant
Side-chain reactant
14
Catalytic propensities
12
10
8
6
4
2
0
Gly
Ala
Val Leu
Ile
Phe Pro Met Trp Ser Thr Cys Tyr Asn Gln Asp Glu Lys Arg His
Amino acids
CATH – EC Relationships
Numbers of CATH code occurrences per (partial) EC number
Dataset of 31367 function-domain pairs from PDB
c.-.-.-
C
A
3.67
19.3
c.s.-.-
c.s.ss.-
2.62
2.01
1.35
7.51
4.18
1.77
c.s.ss.sn
T
116
16.9
6.72
2.02
H
163
21.1
7.78
2.13
Putative evolutionary units of protein structure (H) and units of enzyme function (c.s.ss.-)
Enzyme evolution (1)
• 7.78 distinct homologous superfamilies
(CATH) per distinct function (c.s.ss.-)
• Average enzymes comprises 1.54 CATH
homologous superfamilies
• 7.78/1.54 = 5.05
• Naively implies that each function has
evolved approximately five times
• But ...
Enzyme evolution (2)
• George et al. (Bioinf. 20, i130, 2004) did
the same thing for SCOP vs. EC
• They found 3.5 SCOP superfamilies per
EC sub-subclass (c.s.ss.-)
• Implies each function has evolved
approximately twice
• Answer is highly method-dependent!
CONCLUSIONS
 Enzyme catalysis exploits a limited area of chemical
space. However, they catalyse almost all the reactions
in the metabolism of all organisms.
 Amino acids with alkyl or aryl side-chains act mainly
as main-chain spectators. Amino acids with chemical
functionality in their side-chains are divided into two
groups, depending on whether or not they can also
exploit their main-chain functionality.
 TyMeS: Types of Mechanism and Structure.
ACKNOWLEDGEMENTS
Cambridge Overseas
Trust
QUESTIONS?
 [email protected]
 MACiE database
Mechanism, Annotation and Classification in
Enzymes.
http://www-mitchell.ch.cam.ac.uk/macie/
Function of catalytic residues
Functionality for amino acids currently supported
in the MACiE
________________________________________________
Activating residue
Proton acceptor
Charge destabiliser
Proton donor
Charge stabiliser
Proton relay
Covalently attached
Radical acceptor
Electrophile
Radical donor
Hydride relay
Radical relay
Hydrogen bond acceptor
Radical stabiliser
Hydrogen bond donor
Spectator
Leaving group
Steric hindrance
Metal ligand
Unknown function
Nucleophile
Unspecified steric role
________________________________________________
Function of catalytic residues
Catalytic
=
propensity
% Occurrence as a catalytic residue
% Total occurrence in the dataset
Number of times occurs as a catalytic residue
% Occurrence as a
=
catalytic residue
Total number of catalytic residues
% Total occurrence Number of times residue occurs in all enzyme sequences
=
in the dataset
Total number of residues in all enzyme sequences