SUPERFAMILY 1.75 HMM library and genome assignments server


S13-like H2TH domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   S13-like H2TH domain [ 81297]
Superfamily:   S13-like H2TH domain [ 46946] (3)
Families:   Ribosomal protein S13 [ 46947]
  Middle domain of MutM-like DNA repair proteins [ 81626] (3)
  Topoisomerase VI-B subunit middle domain [ 81705]


Superfamily statistics
Genomes (3,237) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,699 0 25
Proteins 7,695 0 25


Functional annotation
General category Information
Detailed category Translation

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) cellular aromatic compound metabolic process 0.0001265 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0002619 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 8.863e-08 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 9.531e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0002533 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.3987 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.3672 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.07744 Least Informative Inherited
Biological Process (BP) cellular response to stress 1.004e-08 Moderately Informative Direct
Biological Process (BP) gene expression 0.1812 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.05974 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.18 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.262 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 5.317e-06 Informative Direct
Biological Process (BP) response to DNA damage stimulus 4.143e-13 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0001809 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.09904 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.01009 Informative Inherited
Biological Process (BP) DNA catabolic process 3.855e-06 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0001454 Least Informative Direct
Molecular Function (MF) lyase activity 4.107e-09 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 1.732e-11 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing N-glycosyl compounds 9.58e-09 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.02227 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.5724 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.0022 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1.312e-06 Moderately Informative Direct
Cellular Component (CC) cytosol 0.00622 Moderately Informative Inherited
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic small ribosomal subunit 3.348e-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)Isomerases1Least InformativeInherited
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA-formamidopyrimidine glycosylase0Highly InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect
Yeast Phenotype (YP)morphology0Moderately InformativeDirect
Yeast Phenotype (YP)nutrient utilization0Moderately InformativeDirect
Yeast Phenotype (YP)utilization of carbon source0InformativeDirect
Yeast Phenotype (YP)vegetative growth0InformativeDirect
Yeast Phenotype (YP)heat sensitivity0InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six 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)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0Highly InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0Highly InformativeDirect
Enzyme Commission (EC)DNA topoisomerase (ATP-hydrolyzing)3.577e-14Highly 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 functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationIsomerase1Moderately InformativeInherited
Post-translational modificationGlycosidase0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationTopoisomerase2.161e-11Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010979 SSF46946 Protein matches
Abstract

Ribosomal protein S13 is one of the proteins from the small ribosomal subunit [PubMed12464183]. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. S13 contains thee helices and a beta-hairpin in the core of the protein, which form a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension.

This H2TH motif can be found in other proteins as well. In the DNA repair protein, MutM (formamidopyrimidine DNA glycosylase; Fpg), the middle domain contains the H2TH motif. MutM is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidatively damaged bases (N-glycosylase activity) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity) [PubMed10921868]. Other repair enzymes, such as Escherichia coli Endonuclease VIII that excises oxidized pyrimidines from DNA, also contain a DNA-binding H2TH motif within the middle domain. The H2TH domains of these repair proteins are only peripherally involved in binding DNA; their primary function may be simply to position the N-terminal lobe and C-terminal zinc finger domain of the glycosylases for interactions with DNA.

The middle domain of topoisomerase IV-B subunit contains a H2TH motif that is structurally related to the DNA repair proteins. Although the H2TH domain appears to be retained in all archaeal and plant typeż IIB topoisomerases identified to date, it has no known function and has not been observed in other topoisomerase families [PubMed12505993].


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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · 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 9 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 S13-like H2TH 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 9 hidden Markov models representing the S13-like H2TH 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]