DB code: D00828

CATH domain 3.40.50.1400 : Rossmann fold
3.40.50.1400 : Rossmann fold Catalytic domain
E.C. 4.99.1.3
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.1400 : Rossmann fold S00842 D00450

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q05592 Sirohydrochlorin cobaltochelatase
EC 4.99.1.3
NP_460970.1 (Protein)
NC_003197.1 (DNA/RNA sequence)
PF06180 (CbiK)
[Graphical View]
Q72EC8 Sirohydrochlorin cobaltochelatase CbiKP
EC 4.99.1.3
Sirohydrochlorin ferrochelatase CbiKP
EC 4.99.1.4
YP_009872.1 (Protein)
NC_002937.3 (DNA/RNA sequence)
PF06180 (CbiK)
[Graphical View]

KEGG enzyme name
Sirohydrochlorin cobaltochelatase
CbiK
Aanaerobic cobalt chelatase
Cobaltochelatase [ambiguous]
Sirohydrochlorin cobalt-lyase (incorrect)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q72EC8 CBIKP_DESVH Cobalt-sirohydrochlorin + 2 H(+) = sirohydrochlorin + Co(2+). Siroheme + 2 H(+) = sirohydrochlorin + Fe(2+). Homotetramer, dimer of dimers. Periplasm.
Q05592 CBIK_SALTY Sirohydrochlorin + Co(2+) = cobalt-sirohydrochlorin + 2 H(+). Homotrimer.

KEGG Pathways
Map code Pathways E.C.
MAP00860 Porphyrin and chlorophyll metabolism

Compound table
Substrates Products Intermediates
KEGG-id C05778 C00175 C11538 C00080
E.C.
Compound Sirohydrochlorin Co2+ Cobalt-sirohydrochlorin H+
Type amine group,aromatic ring (with nitrogen atoms),carboxyl group heavy metal amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal others
ChEBI 18023
48828
52491
15378
PubChem 104729
46173785
1038
1qgoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xwpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xvxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xvzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1qgoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xwpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SIR
2xvxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xvzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CO Unbound

Reference for Active-site residues
resource references E.C.
literature [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1qgoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2xwpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2xvxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2xvzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qgoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 145;GLU 175;HIS 207 HIS 145;GLU 175;HIS 207(cobalt binding)
2xwpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 145;GLU 175;HIS 207 HIS 145;GLU 175;HIS 207(cobalt binding)
2xvxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 154;GLU 184;HIS 216 HIS 154;GLU 184;HIS 216(cobalt binding)
2xvzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 154;GLU 184;HIS 216 HIS 154;GLU 184;HIS 216(cobalt binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[9]
p.101

References
[1]
Resource
Comments CHARACTERIZATION.
Medline ID
PubMed ID 9150215
Journal J Bacteriol
Year 1997
Volume 179
Pages 3202-12
Authors Raux E, Thermes C, Heathcote P, Rambach A, Warren MJ
Title A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), MUTAGENESIS OF GLU-89; HIS-145; GLU-175; HIS-207 AND ASP-211.
Medline ID
PubMed ID 10451360
Journal Biochemistry
Year 1999
Volume 38
Pages 10660-9
Authors Schubert HL, Raux E, Wilson KS, Warren MJ
Title Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis.
Related PDB 1qgo
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 11215515
Journal Cell Mol Life Sci
Year 2000
Volume 57
Pages 1880-93
Authors Raux E, Schubert HL, Warren MJ
Title Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 11007789
Journal J Biol Chem
Year 2000
Volume 275
Pages 40316-23
Authors Roper JM, Raux E, Brindley AA, Schubert HL, Gharbia SE, Shah HN, Warren MJ
Title The enigma of cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 12196144
Journal Biochem Soc Trans
Year 2002
Volume 30
Pages 595-600
Authors Schubert HL, Raux E, Matthews MA, Phillips JD, Wilson KS, Hill CP, Warren MJ
Title Structural diversity in metal ion chelation and the structure of uroporphyrinogen III synthase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 12758040
Journal Green or red: what stops the traffic in the tetrapyrrole pathway? Trends Plant Sci
Year 2003
Volume 8
Pages 224-30
Authors Cornah JE, Terry MJ, Smith AG
Title
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 12869542
Journal J Biol Chem
Year 2003
Volume 278
Pages 41148-59
Authors Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS
Title Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 18457416
Journal Biochemistry
Year 2008
Volume 47
Pages 5851-7
Authors Lobo SA, Brindley AA, Romao CV, Leech HK, Warren MJ, Saraiva LM
Title Two distinct roles for two functional cobaltochelatases (CbiK) in Desulfovibrio vulgaris hildenborough.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 21173279
Journal Proc Natl Acad Sci U S A
Year 2011
Volume 108
Pages 97-102
Authors Romao CV, Ladakis D, Lobo SA, Carrondo MA, Brindley AA, Deery E, Matias PM, Pickersgill RW, Saraiva LM, Warren MJ
Title Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization.
Related PDB 2xwq 2xws 2xwp 2xvx 2xvz
Related UniProtKB

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.

Created Updated
2009-11-06 2011-11-07