SUPERFAMILY 1.75 HMM library and genome assignments server


N-terminal domain of MutM-like DNA repair proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   N-terminal domain of MutM-like DNA repair proteins [ 81625]
Superfamily:   N-terminal domain of MutM-like DNA repair proteins [ 81624]
Families:   N-terminal domain of MutM-like DNA repair proteins [ 81623] (3)


Superfamily statistics
Genomes (2,256) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,351 18,843 13
Proteins 3,345 18,834 13


Functional annotation
General category Information
Detailed category DNA replication/repair

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) heterocycle metabolic process 3.465e-11 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 4.479e-11 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.355e-10 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 5.962e-10 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 6.15e-09 Least Informative Direct
Biological Process (BP) response to stimulus 8.234e-07 Least Informative Direct
Biological Process (BP) single-organism cellular process 6.968e-05 Least Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 0.0004433 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.001106 Moderately Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 8.55e-06 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 2.105e-05 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.001832 Informative Inherited
Biological Process (BP) DNA catabolic process 1.126e-08 Highly Informative Direct
Molecular Function (MF) hydrolase activity 5.951e-06 Least Informative Direct
Molecular Function (MF) binding 0.03743 Least Informative Inherited
Molecular Function (MF) lyase activity 2.371e-10 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1.041e-06 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 1.705e-12 Informative Direct
Molecular Function (MF) DNA binding 4.194e-08 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing N-glycosyl compounds 2.475e-09 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 3.268e-05 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0InformativeDirect
Enzyme Commission (EC)DNA-formamidopyrimidine glycosylase0Highly InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0Highly InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationGlycosidase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR012319 SSF81624 Protein matches
Abstract

Most damage to bases in DNA is repaired by the base excision repair pathway [PubMed15588838]. The repair is initiated by DNA glycosylases, enzymes that recognise specific lesion bases in DNA and remove them. Formamidopyrimidine-DNA glycosylase (gene fpg) [PubMed7704272] is a bacterial DNA glycosylase that recognises and removes damaged bases with a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Excision of the oxidized guanine occurs via nucleophilic substitution at C1' by the N-terminal proline. The aminal intermediate thus formed rearranges to the Schiff base, which subsequently undergoes beta- and delta-elimination, resulting in complete removal of the lesion nucleoside from DNA. FPG has thus also a nicking activity that cleaves both the 3'- and 5'-phosphodiester bonds at the apurinic/apyrimidinic site, leaving a gap in the DNA that has phosphate groups on both the 5'- and 3'-ends [PubMed15102448].

The protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82) [PubMed11912217]. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger [PubMed12055620].


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 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 N-terminal domain of MutM-like DNA repair proteins 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 N-terminal domain of MutM-like DNA repair proteins 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 ]