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Homocysteine S-methyltransferase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   Homocysteine S-methyltransferase [ 82282]
Families:   Homocysteine S-methyltransferase [ 82283] (2)

Superfamily statistics
Genomes (1,701) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,858 7,074 3
Proteins 2,833 7,048 3

 Functional annotation
General category Metabolism
Detailed category Transferases

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)nitrogen compound metabolic process0.0008250.0002734Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.0020299.882e-05Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process7.752e-070Moderately InformativeDirect
Biological Process (BP)sulfur amino acid metabolic process8.018e-110InformativeDirect
Molecular Function (MF)transferase activity0.00078351.268e-09Least InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups3.854e-080InformativeDirect
Molecular Function (MF)methyltransferase activity2.651e-080Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) nitrogen compound metabolic process 0.0002734 Least Informative Direct
Biological Process (BP) single-organism metabolic process 9.882e-05 Least Informative Direct
Biological Process (BP) biosynthetic process 0.02256 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.194e-05 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0001838 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.001982 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 5.586e-06 Informative Direct
Biological Process (BP) amine biosynthetic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 4.056e-09 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.001016 Informative Inherited
Molecular Function (MF) transferase activity 1.268e-09 Least Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) methyltransferase activity 0 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)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Methionine synthase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Methionine synthase0Highly InformativeDirect

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antidotes0Moderately InformativeDirect
Drugbank ATC_code (DB)methionine0Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
DomainRepeat6.61e-10Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Molecular functionCobalamin0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism3.352e-14Moderately InformativeDirect
UniPathway (UP)amine and polyamine degradation0InformativeDirect
UniPathway (UP)L-methionine biosynthesis0InformativeDirect
UniPathway (UP)betaine degradation0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR003726 SSF82282 Protein matches
Abstract S-methylmethionine: homocysteine methyltransferase from Escherichia coli accepts selenohomocysteine as a substrate. S-methylmethionine is an abundant plant product that can be utilised for methionine biosynthesis [PubMed9882684]. Human methionine synthase (5-methyltetrahydrofolate:L-homocysteine S-transmethylase) shares 53 and 63% identity with the E. coli and the presumptive Caenorhabditis elegans proteins, respectively, and contains all residues implicated in B12 binding to the E. coli protein [PubMed9013615]. Betaine--homocysteine S-methyltransferase converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline [PubMed8798461].

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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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 3 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 Homocysteine S-methyltransferase 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 3 hidden Markov models representing the Homocysteine S-methyltransferase 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.