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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 (1,076) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,972 8,070 13
Proteins 1,929 7,957 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) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000000009364 Least Informative Direct
Biological Process (BP) response to stimulus 0.0001679 Least Informative Direct
Biological Process (BP) biosynthetic process 0.7247 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.1065 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.8595 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.9231 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) double-strand break repair 0.1092 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000000008458 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.00000003897 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) DNA-directed DNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000358 Least 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processMeiosis0InformativeDirect
Biological processDNA replication0.0000000000000898InformativeDirect
Biological processDNA synthesis0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0.000004221Moderately InformativeDirect
Molecular functionSodium0.0000000007438InformativeDirect
Post-translational modificationTransferase0.0000000706Least InformativeDirect
Post-translational modificationHydrolase0.0001336Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease0.000000000000001317Moderately InformativeDirect
Post-translational modificationLyase0.000000743Moderately InformativeDirect
Post-translational modificationDNA-binding0.000001399Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0.0000000000001012Highly InformativeDirect
Post-translational modificationMethylation0.0001403Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0003762Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]