DB code: D00828

CATH domain	3.40.50.1400 : Rossmann fold
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	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
Q05592	CBIK_SALTY	Sirohydrochlorin + Co(2+) = cobalt-sirohydrochlorin + 2 H(+).	Homotrimer.
Q72EC8	CBIKP_DESVH	Cobalt-sirohydrochlorin + 2 H(+) = sirohydrochlorin + Co(2+). Siroheme + 2 H(+) = sirohydrochlorin + Fe(2+).	Homotetramer, dimer of dimers.	Periplasm.

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 18023	48828 48828	52491 52491	15378 15378
PubChem		104729 104729	46173785 46173785	1038 1038

1qgoA01	Unbound	Unbound	Unbound
2xwpA01	Unbound	Unbound	Unbound
2xvxA01	Unbound	Unbound	Unbound
2xvzA01	Unbound	Unbound	Unbound
1qgoA02	Unbound	Unbound	Unbound
2xwpA02	Unbound	Unbound	Bound:SIR
2xvxA02	Unbound	Unbound	Unbound
2xvzA02	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
2xwpA01
2xvxA01
2xvzA01
1qgoA02	HIS 145;GLU 175;HIS 207	HIS 145;GLU 175;HIS 207(cobalt binding)
2xwpA02	HIS 145;GLU 175;HIS 207	HIS 145;GLU 175;HIS 207(cobalt binding)
2xvxA02	HIS 154;GLU 184;HIS 216	HIS 154;GLU 184;HIS 216(cobalt binding)
2xvzA02	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.

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