SUPERFAMILY 1.75 HMM library and genome assignments server


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 (1,805) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,843 20,330 12
Proteins 4,843 20,328 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) nitrogen compound metabolic process 0.1557 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1195 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 7.514e-06 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 9.92e-08 Moderately Informative Direct
Biological Process (BP) sulfur amino acid metabolic process 7.529e-11 Informative Direct
Molecular Function (MF) isomerase activity 2.576e-08 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 1.695e-12 Informative Direct
Molecular Function (MF) methyltransferase activity 7.563e-13 Highly Informative Direct
Molecular Function (MF) intramolecular transferase activity 2.327e-15 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8643 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1729 Least Informative Inherited

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 groups2.219e-10Least InformativeDirect
Enzyme Commission (EC)Methyltransferases5.801e-13Moderately InformativeDirect
Enzyme Commission (EC)Transferring other groups2.862e-11InformativeDirect
Enzyme Commission (EC)Methionine synthase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups3.715e-10Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)0InformativeDirect
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 biosynthesis9.441e-08Moderately InformativeDirect
Biological processMethanogenesis0Highly InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
DomainRepeat3.728e-14Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionS-adenosyl-L-methionine2.624e-11InformativeDirect
Molecular functionCobalamin0Highly InformativeDirect
Post-translational modificationTransferase0.1433Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationMethyltransferase1.564e-13InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism2.268e-07Least InformativeDirect
UniPathway (UP)one-carbon metabolism0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism3.117e-15Moderately InformativeDirect
UniPathway (UP)amino-acid degradation3.911e-06Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0.01862Moderately InformativeInherited
UniPathway (UP)L-glutamate metabolism0InformativeDirect
UniPathway (UP)fermentation0InformativeDirect
UniPathway (UP)methanogenesis0InformativeDirect
UniPathway (UP)L-methionine biosynthesis0InformativeDirect
UniPathway (UP)metabolic intermediate degradation5.688e-12InformativeDirect
UniPathway (UP)L-glutamate degradation0Highly InformativeDirect
UniPathway (UP)methanogenesis from methylated amine0Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation0Highly InformativeDirect

Document: UP 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]