SUPERFAMILY 1.75 HMM library and genome assignments server


5' to 3' exonuclease, C-terminal subdomain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   5' to 3' exonuclease, C-terminal subdomain [ 47807]
Families:   5' to 3' exonuclease, C-terminal subdomain [ 47808] (4)


Superfamily statistics
Genomes (3,202) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,193 0 12
Proteins 6,185 0 12


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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.434e-10 Least Informative Direct
Biological Process (BP) single-organism cellular process 4.245e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.7922 Least Informative Inherited
Biological Process (BP) developmental process 0.4418 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.7859 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 7.195e-10 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 1.062e-08 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.2364 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.06186 Moderately Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to light stimulus 1.771e-10 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 5.626e-09 Informative Direct
Biological Process (BP) growth 0.0006793 Informative Direct
Biological Process (BP) response to UV 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0 Highly Informative Direct
Biological Process (BP) aging 5.169e-08 Highly Informative Direct
Biological Process (BP) DNA replication 0.0006024 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.3489 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1.482e-07 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0001742 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) magnesium ion binding 2.714e-10 Informative Direct
Molecular Function (MF) DNA binding 2.965e-10 Informative Direct
Molecular Function (MF) transition metal ion binding 0.02294 Informative Inherited
Molecular Function (MF) manganese ion binding 3.819e-13 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0772 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)hematopoietic system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)premature death0InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.001375Least InformativeInherited
Worm Phenotype (WP)organism stress response variant1.204e-05InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon 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 phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processDNA excision1.811e-07Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionPotassium0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase1.908e-10Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationEndonuclease4.432e-16InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008918 SSF47807 Protein matches
Abstract

The helix-hairpin-helix (HhH) motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins. The HhH motif is similar to, but distinct from, the helix-turn-helix (HtH) and the helix-loop-helix (HLH) motifs. All three motifs have two helices (H1 and H2) connected by a short turn. DNA-binding proteins with a HhH structural motif are involved in non-sequence-specific DNA binding that occurs via the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups. These HhH motifs are observed in DNA repair enzymes and in DNA polymerases. By contrast, proteins with a HtH motif bind DNA in a sequence-specific manner through the binding of H2 with the major groove; these proteins are primarily gene regulatory proteins. DNA-binding proteins with the HLH structural motif are transcriptional regulatory proteins and are principally related to a wide array of developmental processes [PubMed15356290].

Examples of proteins that contain a HhH motif include the 5'-exonuclease domains of prokaryotic DNA polymerases [PubMed10666572], the eukaryotic/prokaryotic RAD2 family of 5'-3' exonulceases such as T4 RNase H and T5 [PubMed8674116, PubMed9874768], eukaryotic 5' endonucleases such as FEN-1 (Flap) [PubMed9699635], and some viral exonucleases.


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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 8 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 5' to 3' exonuclease, C-terminal subdomain 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 8 hidden Markov models representing the 5' to 3' exonuclease, C-terminal subdomain 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]