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5  structures 758  species 0  interactions 1042  sequences 11  architectures

Family: CbiK (PF06180)

Summary: Cobalt chelatase (CbiK)

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Cobalt chelatase (CbiK) Provide feedback

This family consists of several bacterial cobalt chelatase (CbiK) proteins ( EC:4.99.1.-).

Literature references

  1. Raux E, Thermes C, Heathcote P, Rambach A, Warren MJ; , J Bacteriol 1997;179:3202-3212.: A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis. PUBMED:9150215 EPMC:9150215

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010388

This group, typified by Salmonella typhimurium CbiK, contains anaerobic cobalt chelatases that act in the anaerobic cobalamin biosynthesis pathway [ PUBMED:9150215 , PUBMED:11215515 ].

Cobalamin (vitamin B12) can be complexed with metal via ATP-dependent reactions (aerobic pathway) (e.g., in Pseudomonas denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in S. typhimurium) [ PUBMED:8905078 , PUBMED:11469861 ]. The corresponding cobalt chelatases are not homologous. This group belongs to the class of ATP-independent, single-subunit chelatases that also includes distantly related protoporphyrin IX (PPIX) ferrochelatase (HemH) (Class II chelatases) [ PUBMED:12686546 ]. The structure of S. typhimurium CbiK shows that it has a remarkably similar topology to Bacillus subtilis ferrochelatase despite only weak sequence conservation [ PUBMED:10451360 ]. Both enzymes contain a histidine residue identified as the metal ion ligand, but CbiK contains a second histidine in place of the glutamic acid residue identified as a general base in PPIX ferrochelatase [ PUBMED:10451360 ]. Site-directed mutagenesis has confirmed a role for this histidine and a nearby glutamic acid in cobalt binding, modulating metal ion specificity as well as catalytic efficiency [ PUBMED:10451360 ].

It should be noted that CysG and Met8p, which are multifunctional proteins associated with siroheme biosynthesis, include chelatase activity and can therefore be considered as the third class of chelatases [ PUBMED:12686546 ]. As with the class II chelatases, they do not require ATP for activity. However, they are not structurally similar to HemH or CbiK, and it is likely that they have arisen by the acquisition of a chelatase function within a dehydrogenase catalytic framework [ PUBMED:11980703 , PUBMED:12686546 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Chelatase (CL0043), which has the following description:

Metallated tetrapyrroles are used as prosthetic groups in proteins involved in biologically important processes such as photosynthesis, oxygen transport, drug metabolism and nitric oxide synthesis. In living organisms, metallation is catalysed by a group of enzymes called chelatases. This clan contains ferrochelatase (heme) and cobalt chelatase [1].

The clan contains the following 7 members:

CbiK CbiX DUF3364 Ferrochelatase Oxidored_nitro Peripla_BP_2 ZnuA


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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_10975 (release 9.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 8
Number in full: 1042
Average length of the domain: 252.50 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 83.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.2 26.2
Noise cut-off 26.1 26.1
Model length: 262
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CbiK domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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