SUPERFAMILY 1.75 HMM library and genome assignments server


Methionine synthase activation domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Methionine synthase activation domain-like [ 56506]
Superfamily:   Methionine synthase activation domain-like [ 56507] (2)
Families:   Methionine synthase SAM-binding domain [ 56508]
  Hypothetical protein TM0269 [ 75590]


Superfamily statistics
Genomes (1,519) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,661 4,193 4
Proteins 1,650 4,189 4


Functional annotation
General category Metabolism
Detailed category Amino acids 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 6.367e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 8.874e-06 Least Informative Direct
Biological Process (BP) biosynthetic process 0.003585 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 1.069e-12 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 9.974e-11 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 7.95e-05 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0003416 Moderately Informative Direct
Biological Process (BP) sulfur amino acid metabolic process 0 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 2.92e-13 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 1.873e-11 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 5.228e-07 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 2.947e-14 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

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Molecular functionCobalamin0Highly InformativeDirect
Post-translational modificationTransferase1.729e-14Least InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR004223 SSF56507 Protein matches
Abstract

Vitamin B12 dependent methionine synthase (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin.

In Escherichia coli, methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate, the third module binds the B12 cofactor , and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain [PubMed11731805]. The activation domain adopts an unusual alpha/beta fold.


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) ]

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 2 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 Methionine synthase activation domain-like 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 2 hidden Markov models representing the Methionine synthase activation domain-like 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) · Internal database links ]