EzCatDB: D00828
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DB codeD00828
CATH domainDomain 13.40.50.1400 : Rossmann fold
Domain 23.40.50.1400 : Rossmann foldCatalytic domain
E.C.4.99.1.3

CATH domainRelated DB codes (homologues)
3.40.50.1400 : Rossmann foldS00842,D00450

Enzyme Name
UniProtKBKEGG

Q05592Q72EC8
Protein nameSirohydrochlorin cobaltochelataseSirohydrochlorin cobaltochelatase CbiKPSirohydrochlorin cobaltochelatase
CbiK
Aanaerobic cobalt chelatase
Cobaltochelatase [ambiguous]
Sirohydrochlorin cobalt-lyase (incorrect)
SynonymsEC 4.99.1.3
EC 4.99.1.3
Sirohydrochlorin ferrochelatase CbiKP
EC 4.99.1.4
RefSeqNP_460970.1 (Protein)
NC_003197.1 (DNA/RNA sequence)
YP_009872.1 (Protein)
NC_002937.3 (DNA/RNA sequence)
PfamPF06180 (CbiK)
[Graphical view]
PF06180 (CbiK)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00860Porphyrin and chlorophyll metabolism

UniProtKB:Accession NumberQ05592Q72EC8
Entry nameCBIK_SALTYCBIKP_DESVH
ActivitySirohydrochlorin + Co(2+) = cobalt-sirohydrochlorin + 2 H(+).Cobalt-sirohydrochlorin + 2 H(+) = sirohydrochlorin + Co(2+).,Siroheme + 2 H(+) = sirohydrochlorin + Fe(2+).
SubunitHomotrimer.Homotetramer, dimer of dimers.
Subcellular location
Periplasm.
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
            
1qgoA01UnboundUnboundUnbound 
2xwpA01UnboundUnboundUnbound 
2xvxA01UnboundUnboundUnbound 
2xvzA01UnboundUnboundUnbound 
1qgoA02UnboundUnboundUnbound 
2xwpA02UnboundUnboundBound:SIR 
2xvxA02UnboundUnboundUnbound 
2xvzA02UnboundBound:_COUnbound 

Active-site residues
resource
literature [2]
pdbCatalytic residuesCofactor-binding residues
          
1qgoA01 
 
2xwpA01 
 
2xvxA01 
 
2xvzA01 
 
1qgoA02HIS 145;GLU 175;HIS 207
HIS 145;GLU 175;HIS 207(cobalt binding)
2xwpA02HIS 145;GLU 175;HIS 207
HIS 145;GLU 175;HIS 207(cobalt binding)
2xvxA02HIS 154;GLU 184;HIS 216
HIS 154;GLU 184;HIS 216(cobalt binding)
2xvzA02HIS 154;GLU 184;HIS 216
HIS 154;GLU 184;HIS 216(cobalt binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[9]p.101

references
[1]
CommentsCHARACTERIZATION.
PubMed ID9150215
JournalJ Bacteriol
Year1997
Volume179
Pages3202-12
AuthorsRaux E, Thermes C, Heathcote P, Rambach A, Warren MJ
TitleA role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), MUTAGENESIS OF GLU-89; HIS-145; GLU-175; HIS-207 AND ASP-211.
PubMed ID10451360
JournalBiochemistry
Year1999
Volume38
Pages10660-9
AuthorsSchubert HL, Raux E, Wilson KS, Warren MJ
TitleCommon chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis.
Related PDB1qgo
[3]
PubMed ID11215515
JournalCell Mol Life Sci
Year2000
Volume57
Pages1880-93
AuthorsRaux E, Schubert HL, Warren MJ
TitleBiosynthesis of cobalamin (vitamin B12): a bacterial conundrum.
[4]
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.
[5]
PubMed ID12196144
JournalBiochem Soc Trans
Year2002
Volume30
Pages595-600
AuthorsSchubert HL, Raux E, Matthews MA, Phillips JD, Wilson KS, Hill CP, Warren MJ
TitleStructural diversity in metal ion chelation and the structure of uroporphyrinogen III synthase.
[6]
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
[7]
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.
[8]
PubMed ID18457416
JournalBiochemistry
Year2008
Volume47
Pages5851-7
AuthorsLobo SA, Brindley AA, Romao CV, Leech HK, Warren MJ, Saraiva LM
TitleTwo distinct roles for two functional cobaltochelatases (CbiK) in Desulfovibrio vulgaris hildenborough.
[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 (CbiK) is evolutionarily related to CbiXs (S00842 in EzCatDB), which has a single domain forming a homodimer (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]).
(1) The binding of cobalt to the active site of this enzyme (His145, His207 and Glu175 in 1qgo) facilitates the desolvation step.
(2) The cobalt ion is displaced from the binding site by the introduction of the SHC acetate group, inducing the conformational change both the active site and the tetra-pyrrole molecule.
(3) Either one of both of the histidine residues acting as general bases, to deprotonate the pyrroles, leading to the formation of a nitrogen-cobalt chelation.

createdupdated
2009-11-062011-11-07


Copyright: Nozomi Nagano, JST & CBRC-AIST
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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 - )
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