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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1kyq
Original Entry
Title:
Oxidoreductase, lyase
Compound:
Siroheme biosynthesis protein met8
Mutant:
No
UniProt/Swiss-Prot:
P15807-MET8_YEAST
EC Class:
1.-.-.-
Other CSA Entries:
Overview of all sites for 1kyq
Homologues of 1kyq
Entries for UniProt/Swiss-Prot: P15807
Entries for EC: 1.-.-.-
Other Databases:
PDB entry: 1kyq
PDBsum entry: 1kyq
UniProt/Swiss-Prot: P15807
IntEnz entry: 1.-.-.-
Literature Report:
Introduction:
Biosynthesis of the sirohaem cofactor is completed by Met8p, by a beta-NAD+-dependent dehydrogenation of precorrin-2 to produce sirohydrochlorin, followed by ferrochelation to generate sirohaem. Met8p has a similar role in cobalamin biosynthesis.
Mechanism:
NAD-dependent dehydrogenation occurs by Asp 141 functioning as a catalytic general base to abstract a proton from the pyrrole nitrogen of ring C with concomitant hydride transfer from the prochiral bridge carbon to the nicotinamide ring of NAD.

During ferrochelation Asp 141 again acts as a general base to remove additional protons from the pyrrole nitrogens during metal ion insertion.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
800 0
NucleophileSubstrate
It accepts a hydride in the reaction.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11980703 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 141 141Sidechain
Acid/baseSubstrate
Asp 141 functions as a general base in both dehydrogenase and chelatase reactions by abstraction of protons from pyrrole nitrogens.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11980703 Current protein Conservation of residue
PubMed ID 11980703 Current protein Mutagenesis of residue
PubMed ID 11980703 Current protein Residue is positioned appropriately (ligand position known)
References:
1
The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase.
H. L. Schubert and E. Raux and A. A. Brindley and H. K. Leech and K. S. Wilson and C. P. Hill and M. J. Warren
EMBO J 21, (9) 2068-75, (2002).
11980703
2
Production of cobalamin and sirohaem in Bacillus megaterium: an investigation into the role of the branchpoint chelatases sirohydrochlorin ferrochelatase (SirB) and sirohydrochlorin cobalt chelatase (CbiX).
H. K. Leech and E. Raux-Deery and P. Heathcote and M. J. Warren
Biochem Soc Trans 30, (4) 610-3, (2002).
12196147
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