DB code: S00842

CATH domain 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 D00450 D00828

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
O29537 Sirohydrochlorin cobaltochelatase
EC 4.99.1.3
CbiXS
NP_069555.1 (Protein)
NC_000917.1 (DNA/RNA sequence)
PF01903 (CbiX)
[Graphical View]

KEGG enzyme name
Sirohydrochlorin cobaltochelatase
CbiX
CbiXS
Anaerobic cobalt chelatase
Cobaltochelatase [ambiguous]
Sirohydrochlorin cobalt-lyase (incorrect)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
O29537 CBIX_ARCFU Sirohydrochlorin + Co(2+) = cobalt-sirohydrochlorin + 2 H(+). Tetramer.

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
1tjnA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2dj5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2dj5B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xwqA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SIR
2xwqB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xwqC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SIR
2xwqD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2xwsA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1tjnA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74
2dj5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74
2dj5B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74
2xwqA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74
2xwqB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74
2xwqC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74
2xwqD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74
2xwsA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; HIS 74

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[7]
Fig.1, p.38

References
[1]
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
[2]
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
[3]
Resource
Comments
Medline ID
PubMed ID 12408752
Journal Biochem J
Year 2003
Volume 370
Pages 505-16
Authors Raux E, Leech HK, Beck R, Schubert HL, Santander PJ, Roessner CA, Scott AI, Martens JH, Jahn D, Thermes C, Rambach A, Warren MJ
Title Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium.
Related PDB
Related UniProtKB
[4]
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
[5]
Resource
Comments
Medline ID
PubMed ID 12686546
Journal J Biol Chem
Year 2003
Volume 278
Pages 22388-95
Authors Brindley AA, Raux E, Leech HK, Schubert HL, Warren MJ
Title A story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea.
Related PDB
Related UniProtKB
[6]
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
[7]
Resource
Comments
Medline ID
PubMed ID 16835730
Journal J Struct Funct Genomics
Year 2006
Volume 7
Pages 37-50
Authors Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN
Title Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus.
Related PDB 1tjn 2dj5
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 17584754
Journal Protein Eng Des Sel
Year 2007
Volume 20
Pages 257-65
Authors Pisarchik A, Petri R, Schmidt-Dannert C
Title Probing the structural plasticity of an archaeal primordial cobaltochelatase CbiX(S).
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 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]).

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