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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 2018_03 genome PDB chains (SCOP 1.75)
Domains 1,972 10,331 13
Proteins 1,929 10,206 13


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

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)immune system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)hematopoietic system phenotype0.036Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.2068Least InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.0007232Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.003404Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.00446Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.005857Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.006165Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B cell differentiation0.000005109InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.00000558InformativeDirect
Mammalian Phenotype (MP)abnormal immunoglobulin V(D)J recombination0.000000000009737Highly InformativeDirect

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)testis0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0.00000000000006453InformativeDirect

Document: EC 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]