EzCatDB: S00842
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00842
CATH domainDomain 13.40.50.1400 : Rossmann foldCatalytic domain
E.C.4.99.1.3

CATH domainRelated DB codes (homologues)
3.40.50.1400 : Rossmann foldD00450,D00828

Enzyme Name
UniProtKBKEGG

O29537
Protein nameSirohydrochlorin cobaltochelataseSirohydrochlorin cobaltochelatase
CbiX
CbiXS
Anaerobic cobalt chelatase
Cobaltochelatase [ambiguous]
Sirohydrochlorin cobalt-lyase (incorrect)
SynonymsEC 4.99.1.3
CbiXS
RefSeqNP_069555.1 (Protein)
NC_000917.1 (DNA/RNA sequence)
PfamPF01903 (CbiX)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00860Porphyrin and chlorophyll metabolism

UniProtKB:Accession NumberO29537
Entry nameCBIX_ARCFU
ActivitySirohydrochlorin + Co(2+) = cobalt-sirohydrochlorin + 2 H(+).
SubunitTetramer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC05778C00175C11538C00080
CompoundSirohydrochlorinCo2+Cobalt-sirohydrochlorinH+
Typeamine group,aromatic ring (with nitrogen atoms),carboxyl groupheavy metalamine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metalothers
ChEBI18023
48828
52491
15378
PubChem
104729
46173785
1038
            
1tjnA00UnboundUnboundUnbound 
2dj5A00UnboundUnboundUnbound 
2dj5B00UnboundUnboundUnbound 
2xwqA00UnboundUnboundBound:SIR 
2xwqB00UnboundUnboundUnbound 
2xwqC00UnboundUnboundBound:SIR 
2xwqD00UnboundUnboundUnbound 
2xwsA00UnboundUnboundUnbound 

Active-site residues
resource
literature [7]
pdbCatalytic residues
         
1tjnA00HIS 10; HIS 74
2dj5A00HIS 10; HIS 74
2dj5B00HIS 10; HIS 74
2xwqA00HIS 10; HIS 74
2xwqB00HIS 10; HIS 74
2xwqC00HIS 10; HIS 74
2xwqD00HIS 10; HIS 74
2xwsA00HIS 10; HIS 74

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]Fig.1, p.38

references
[1]
PubMed ID11215515
JournalCell Mol Life Sci
Year2000
Volume57
Pages1880-93
AuthorsRaux E, Schubert HL, Warren MJ
TitleBiosynthesis of cobalamin (vitamin B12): a bacterial conundrum.
[2]
PubMed ID11007789
JournalJ Biol Chem
Year2000
Volume275
Pages40316-23
AuthorsRoper JM, Raux E, Brindley AA, Schubert HL, Gharbia SE, Shah HN, Warren MJ
TitleThe enigma of cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway.
[3]
PubMed ID12408752
JournalBiochem J
Year2003
Volume370
Pages505-16
AuthorsRaux E, Leech HK, Beck R, Schubert HL, Santander PJ, Roessner CA, Scott AI, Martens JH, Jahn D, Thermes C, Rambach A, Warren MJ
TitleIdentification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium.
[4]
PubMed ID12758040
JournalGreen or red: what stops the traffic in the tetrapyrrole pathway? Trends Plant Sci
Year2003
Volume8
Pages224-30
AuthorsCornah JE, Terry MJ, Smith AG
Title
[5]
PubMed ID12686546
JournalJ Biol Chem
Year2003
Volume278
Pages22388-95
AuthorsBrindley AA, Raux E, Leech HK, Schubert HL, Warren MJ
TitleA story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea.
[6]
PubMed ID12869542
JournalJ Biol Chem
Year2003
Volume278
Pages41148-59
AuthorsRodionov DA, Vitreschak AG, Mironov AA, Gelfand MS
TitleComparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.
[7]
PubMed ID16835730
JournalJ Struct Funct Genomics
Year2006
Volume7
Pages37-50
AuthorsYin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN
TitleCrystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus.
Related PDB1tjn,2dj5
[8]
PubMed ID17584754
JournalProtein Eng Des Sel
Year2007
Volume20
Pages257-65
AuthorsPisarchik A, Petri R, Schmidt-Dannert C
TitleProbing the structural plasticity of an archaeal primordial cobaltochelatase CbiX(S).
[9]
PubMed ID21173279
JournalProc Natl Acad Sci U S A
Year2011
Volume108
Pages97-102
AuthorsRomao CV, Ladakis D, Lobo SA, Carrondo MA, Brindley AA, Deery E, Matias PM, Pickersgill RW, Saraiva LM, Warren MJ
TitleEvolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization.
Related PDB2xwq,2xws,2xwp,2xvx,2xvz

comments
This enzyme forms a homodimer with a symmetrical active site, which is located at the interface of the two subunits (see [9]). This enzyme (CbiXS) can be an ancestral enzyme of CbiK (D00828 in EzCatDB) (see [9]).
According to the literature [9], this enzyme catalyzes the insertion of cobalt ion into a tetra-pyrrole, sirohydrochlorin (SHC). This reaction involves several steps including removal of water from the metal ion, deprotonation of the tetra-pyrrole nitrogens (see [9]).
The distortion of the tetra-pyrrole during the reaction is smaller than that caused in the homologous enzyme, CbiK (see [9]). The lack of distortion can be compensated by the fact that either face of the bound SHC can be deprotonated. If the cobalt is bound to a subunit of the dimer, then His10 on the other subunit can deprotonate the pyrrole nitrogen. Moreover, a metal-oxygen bond with the propionate group of either A or B ring on SHC might stabilize the metal-insertion reaction (see [9]).

createdupdated
2009-11-062011-11-07
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.