MMechanism, AAnnotation and CClassification iin EEnzymes.http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
The MACiE DatabaseThe MACiE Database
G.L. Holliday et al., Nucl. Acids Res., 35, D515-D520 (2007)
Gemma Holliday, Daniel Almonacid, Noel O’Boyle,
Janet Thornton (EBI), Peter Murray-Rust, Gail Bartlett (EBI),
James Torrance, John Mitchell
Enzyme Nomenclature and Enzyme Nomenclature and ClassificationClassificationEC ClassificationEC Classification
Class
Subclass
Sub-subclass
Serial number
The EC ClassificationThe 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
Only deals with overall reaction
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
MMechanism, AAnnotation and CClassification iin EEnzymes.http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
MACiE DatabaseMACiE Database
Coverage of MACiE
Representative – based on a non-homologous dataset,and chosen to represent each available EC sub-subclass.
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.-.-.-
56 EC 1.2.-.-
184 EC 1.2.3.-
1312 EC 1.2.3.4
MACiE covers:
6 EC 1.-.-.-
53 EC 1.2.-.-
156 EC 1.2.3.-
199 EC 1.2.3.4
Repertoire of Enzyme CatalysisRepertoire of Enzyme Catalysis
G.L. Holliday et al., J. Molec. Biol., 372, 1261-1277 (2007)
G.L. Holliday et al., J. Molec. Biol., accepted (2009)
Repertoire of Enzyme Catalysis
0
20
40
60
80
100
120
140
HeterolyticElimination
HomolyticElimination
ElectrophilicAddition
NucleophilicAddition
HomolyticAddition
ElectrophilicSubstitution
NucleophilicSubstitution
HomolyticSubstitution
Reaction Types
Num
ber
of
step
s in
MA
CiE
Intramolecular
Bimolecular
Unimolecular
Enzyme chemistry is largely nucleophilic
0
50
100
150
200
250
300
350
400
450
Reaction Types
Num
ber
of
ste
ps in M
ACiE
ProtonProtontransfertransfer
AdAdNN22 E1E1 SSNN22 E2E2 RadicalRadicalreactionreaction
Tautom.Tautom. OthersOthers
Repertoire of Enzyme Catalysis
We use a combination of bioinformatics & chemoinformatics to identify similarities between enzyme-catalysed reaction mechanisms
… we align the steps of chemical reactions.
Just like sequence alignment!
We can measure their similarity …
EC is our Functional Classification
Enzyme Commission (EC) Nomenclature, 1992, Academic Press, San Diego, 6th Edition
Chemical reaction
Enzyme catalysis databases
G.L. Holliday et al., Nucleic Acids Res., 35, D515 (2007)
S.C. Pegg et al., Biochemistry, 45, 2545 (2006)
N. Nagano, Nucleic Acids Res., 33, D407 (2005)
Coverage of MACiE
Representative – based on a non-homologous dataset,and chosen to represent each available EC sub-subclass.
Work with domains - evolutionary & structural units of proteins.
Map enzyme catalytic mechanisms to domains to quantify convergent and divergent functional evolution of enzymes.
Domains
Numbers of CATH code occurrences per EC number
C
A
T
H
c.-.-.- c.s.-.- c.s.ss.- c.s.ss.sn
3.17
11.00
28.00
38.33
1.73
3.27
4.89
5.80
1.38
1.93
2.24
2.46
1.11
1.60
1.19
1.22
Results: Convergent Evolution
2.46 CATH/EC reaction
Convergent Evolution
Numbers of CATH code occurrences per EC number
C
A
T
H
c.-.-.- c.s.-.- c.s.ss.- c.s.ss.sn
3.17
11.00
28.00
38.33
1.73
3.27
4.89
5.80
1.38
1.93
2.24
2.46
1.11
1.60
1.19
1.22
Results: Convergent Evolution
2.46 CATH/EC reaction: Convergent EvolutionAn average reaction has evolved independently in 2.46 superfamilies
EC reactions/CATH
C4.75
19.50
39.25
90.00
c.-.-.-c.-.-.-
c.s.-.-c.s.-.-
c.s.ss.-
c.s.ss.sn
A3.14
7.00
10.48
17.90
T1.36
1.79
2.08
3.05
H1.20
1.36
1.462.05
database entries/CATH
2.18
Results: Divergent Evolution
1.46 EC reactions/CATH Divergent Evolution
EC reactions/CATH
C4.75
19.50
39.25
90.00
c.-.-.-c.-.-.-
c.s.-.-c.s.-.-
c.s.ss.-
c.s.ss.sn
A3.14
7.00
10.48
17.90
T1.36
1.79
2.08
3.05
H1.20
1.36
1.462.05
database entries/CATH
2.18
Results: Divergent Evolution
1.46 EC reactions/CATH: Divergent EvolutionAn average superfamily has evolved 1.46 different reactions
Now we want to evolve chemical reactions in silico across chemical, or EC, space.
1. To understand and rationalise convergent and divergent biochemical evolution;
2. To better relate protein structure and function;
3. To understand the influence on networks of coupled reactions.
(2) Understanding Protein Structure
• We seek to understand the influence of folding pathway on protein structure over all time scales (including the evolutionary one).
ACKNOWLEDGEMENTSACKNOWLEDGEMENTS
Dr Gemma Holliday
Dr Daniel Almonacid
Dr Noel O’Boyle
Prof. Janet Thornton (EBI)
Dr Peter Murray-Rust
Dr Florian Nigsch