Summary
Cobalt chelatase (CbiK)
This family consists of several bacterial cobalt chelatase (CbiK) proteins ( EC:4.99.1.-).
Literature references
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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
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.
Clan
This family is a member of clan Chelatase (CL0043), which contains the following 3 members:
CbiK CbiX FerrochelataseInternal database links
| SCOOP: | DUF2193 |
External database links
| PANDIT: | PF06180 |
| SCOP: | 1qgo |
| SYSTERS: | CbiK |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Alignments
There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...
View options
Formatting options
Download options
Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.
You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.
External links
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER2.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family. 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 or full alignments.
Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.
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
| Seed source: | Pfam-B_10975 (release 9.0) |
| Previous IDs: | none |
| Type: | Family |
| Author: | Moxon SJ |
| Number in seed: | 8 |
| Number in full: | 235 |
| Average length of the domain: | 250.40 aa |
| Average identity of full alignment: | 36 % |
| Average coverage of the sequence by the domain: | 85.72 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq
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| Model details: |
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| Model length: | 262 | ||||||||||||
| Family (HMM) version: | 4 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
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Structures
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.
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