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15  structures 1546  species 1  interaction 1640  sequences 16  architectures

Family: CbiC (PF02570)

Summary: Precorrin-8X methylmutase

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Precorrin-8X methylmutase Provide feedback

This is a family Precorrin-8X methylmutases also known as Precorrin isomerase, CbiC/CobH, EC:5.4.1.2. This enzyme catalyses the reaction: Precorrin-8X <=> hydrogenobyrinate. This enzyme is part of the Cobalamin (vitamin B12) biosynthetic pathway and catalyses a methyl rearrangement [1,2].

Literature references

  1. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C; , Biochem J 1998;335:159-166.: Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. PUBMED:9742225 EPMC:9742225

  2. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM; , J Bacteriol 1993;175:3303-3316.: Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. PUBMED:8501034 EPMC:8501034


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003722

Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase [PUBMED:12869542]. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase [PUBMED:17163662].

There are at least two distinct cobalamin biosynthetic pathways in bacteria [PUBMED:11153269]:

Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) [PUBMED:11215515]. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.

This entry represents CbiC and CobH precorrin-8X methylmutase (also known as precorrin isomerase, EC), both as stand-alone enzymes and when CobJ forms part of a bifunctional enzyme. CobH and CbiC from the aerobic and anaerobic pathways, respectively, catalyse a methyl rearrangement in precorrin-8 that moves the methyl group from C-11 to C-12 to produce hydrogenobyrinic acid [PUBMED:11470433]. Hydrogenobyrinic acid now contains all the major framework alterations associated with corrin synthesis [PUBMED:11215515].

CobH and CbiC can sometimes be fused to other enzymes in the cobalamin pathway to make bifunctional enzymes: e.g., with CobJ/CibH (precorrin-3B C17-methylase/precorrin isomerase, INTERPRO) and with CbiX (precorrin isomerase, INTERPRO).

Gene Ontology

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Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(155)
Full
(1640)
Representative proteomes NCBI
(1277)
Meta
(315)
RP15
(144)
RP35
(309)
RP55
(396)
RP75
(459)
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Format an alignment

  Seed
(155)
Full
(1640)
Representative proteomes NCBI
(1277)
Meta
(315)
RP15
(144)
RP35
(309)
RP55
(396)
RP75
(459)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(155)
Full
(1640)
Representative proteomes NCBI
(1277)
Meta
(315)
RP15
(144)
RP35
(309)
RP55
(396)
RP75
(459)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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

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 HMMER3.

Pfam alignments:

HMM logo

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Trees

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: COGs
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 155
Number in full: 1640
Average length of the domain: 196.50 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 85.28 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 23.9 29.0
Noise cut-off 20.6 20.2
Model length: 198
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

CbiC

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 CbiC domain has been found. There are 15 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 seqence.

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