SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Cobalamin (vitamin B12)-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Flavodoxin-like [ 52171] (15)
Superfamily:   Cobalamin (vitamin B12)-binding domain [ 52242]
Families:   Cobalamin (vitamin B12)-binding domain [ 52243] (5)


Superfamily statistics
Genomes (1,817) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,880 36,849 12
Proteins 4,880 36,837 12


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0.0001172 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.4586 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.06068 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2368 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000005909 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.00002577 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00000009643 Moderately Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.0000004363 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.000000002507 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.00008722 Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 0.00572 Least Informative Inherited
Molecular Function (MF) isomerase activity 0.000000001021 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00002742 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) tetrapyrrole binding 0.000000000002154 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Molecular Function (MF) vitamin binding 0.0000000000003853 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0000000002219Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0.0000000000005801Moderately InformativeDirect
Enzyme Commission (EC)Transferring other groups0.00000000002862InformativeDirect
Enzyme Commission (EC)Methionine synthase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.000000388Moderately InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
Biological processMethanogenesis0Highly InformativeDirect
DomainRepeat0.00000000000005163Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0000000001141InformativeDirect
Molecular functionCobalamin0Highly InformativeDirect
Post-translational modificationTransferase0.1511Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0.000000000000007572InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006158 SSF52242 Protein matches
Abstract

The cobalamin (vitamin B12) binding domain has an alpha/beta fold that is a common motif found in several different cobalamin-binding proteins. Proteins containing this domain include: methionine synthase; the small subunit of glutamate mutase [PubMed10467146]; the alpha and beta subunits of methylmalonyl-CoA mutase; and mono- and tri-methylamine corrinoid proteins (MMCP and TCP, respectively) [PubMed9642198]. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap ; in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain [PubMed11731805].

The core structure of the cobalamin domain consists of 5 parallel beta-sheets, surrounded by 4-5 alpha helices in three layers, alpha/beta/alpha [PubMed7992050]. The fold of the domain resembles that of the nucleotide-binding proteins (a Rossman fold). Upon binding B12, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 6 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Cobalamin (vitamin B12)-binding domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 6 hidden Markov models representing the Cobalamin (vitamin B12)-binding domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]