SUPERFAMILY 1.75 HMM library and genome assignments server

DNA polymerase beta, N-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   DNA polymerase beta, N-terminal domain-like [ 47802]
Families:   DNA polymerase beta, N-terminal domain-like [ 47803] (3)


Superfamily statistics
Genomes (1,069) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,950 6,625 13
Proteins 1,907 6,539 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) cellular aromatic compound metabolic process 0.0000000002344 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000007408 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000000155 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000000001653 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000001034 Least Informative Direct
Biological Process (BP) biosynthetic process 0.1032 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.03805 Least Informative Inherited
Biological Process (BP) response to stimulus 0.0019 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.00000000001492 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.1667 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.1586 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.006413 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.1502 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.2505 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Molecular Function (MF) transferase activity 0.0000207 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.9084 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000000001968 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.00009294 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.001663 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.0000004615 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) DNA polymerase activity 0.000009013 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0.00000000001048Moderately InformativeDirect
Enzyme Commission (EC)DNA nucleotidylexotransferase0Highly 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)hematopoietic system phenotype0.02992Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.03916Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2108Least InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.0005891Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.00312Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.003992Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.00471Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B cell differentiation0.00002244InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.0009961InformativeDirect
Mammalian Phenotype (MP)abnormal immunoglobulin V(D)J recombination0.00000000002387Highly InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.000008667Highly InformativeDirect

Document: MP 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)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA 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 polymerase0.000000000004963InformativeDirect

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 recombination0InformativeDirect
Biological processMeiosis0InformativeDirect
Biological processDNA replication0.00000000001818InformativeDirect
Biological processDNA synthesis0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionDNA-binding0.0003199Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0.00003834Moderately InformativeDirect
Molecular functionSodium0.0000000001089InformativeDirect
Post-translational modificationTransferase0.000001097Least InformativeDirect
Post-translational modificationHydrolase0.0001011Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease0.000000000000002202Moderately InformativeDirect
Post-translational modificationLyase0.00002157Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0.00000000000486InformativeDirect
Post-translational modificationMethylation0.000001151Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000001983Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010996 SSF47802 Protein matches
Abstract

Mammalian DNA polymerase beta (polB, ) is a 39-kDa protein with both nucleotidyltransferase and 5'-deoxyribose phosphodiesterase activities, playing a role in both excision repair and meiosis. polB has a modular organisation with an 8-kDa N-terminal domain (NTD) connected to the 31-kDa C-terminal domain by a protease-hypersensitive hinge region. The NTD acts as a single-stranded DNA binding domain, interacting most efficiently with the 5'-phosphate of the downstream primer of the gapped DNA. This interaction is mediated by a helix-hairpin-helix motif (HhH), which is also found in several other DNA repair enzymes. The residue threonine 79 (T79), which is located within the NTD, was identified as being critical to polB function, even though it makes no contact with either DNA template or dNTP substrate; T79 is located between two HhH motifs, and acts as a hinge residue that is important for positioning the DNA within the active site [PubMed12121998].

The catalytic core (residues 148-242) of murine terminal deoxynucleotidyl transferase (TdT, ) displays a structural fold that is similar to polB, and shares a common two-metal ion mechanism of nucleotidyl transfer with polB [PubMed11823435]. TdT elongates DNA strands in a template-independent manner, and belongs to the pol X family of polymerases. TdT has only been found in vertebrates, where it is highly conserved. TdT brings additional diversity in the immune repertoire by adding nucleotides, called N regions, to the V(D)J recombination junction sites of immunoglobulin and T-cell receptor genes.


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) · Xenopus Anatomy (XA) · 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 4 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 DNA polymerase beta, N-terminal 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 4 hidden Markov models representing the DNA polymerase beta, N-terminal 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]