Polb DNA polymerase beta [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Polbprovided by RGD
Official Full Name: DNA polymerase betaprovided by RGD
Primary source: RGD:3363
See related: EnsemblRapid:ENSRNOG00000019150 AllianceGenome:RGD:3363
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables DNA-directed DNA polymerase activity; damaged DNA binding activity; and metal ion binding activity. Involved in several processes, including DNA repair; response to gamma radiation; and response to hyperoxia. Predicted to be located in cytoplasm and spindle microtubule. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human POLB (DNA polymerase beta). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Testes (RPKM 203.3), Muscle (RPKM 115.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16q12.5

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (76081903..76105174)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (69379438..69402710)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (74237001..74260272)

Chromosome 16 - NC_086034.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

History of DNA polymerase beta X-ray crystallography.
Title: History of DNA polymerase β X-ray crystallography.
The I260Q variant of DNA polymerase beta is an efficient mutator polymerase with fairly indiscriminate misincorporation activities opposite all template bases.
Title: Structural changes in the hydrophobic hinge region adversely affect the activity and fidelity of the I260Q mutator DNA polymerase β.
The closed state of E295K has a more distorted active site than the active site in the wild-type Polb.
Title: Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway.
decline in pol beta activity started between 30 and 45 days postnatal in all the tissues. Post mitotic tissues showed pronounced decline than the proliferating tissues
Title: Age-related decline in DNA polymerase β activity in rat brain and tissues.
at low pH the chemical step is rate limiting for catalysis, but at high pH, a postchemistry conformational step is rate limiting due to a pH-dependent increase in the rate of nucleotidyl transfer
Title: Kinetic mechanism of active site assembly and chemical catalysis of DNA polymerase β.
These results point to the hinge region of DNA polymerase beta as being critical in the maintenance of the proper geometry of the dNTP binding pocket.
Title: Hinge residue I174 is critical for proper dNTP selection by DNA polymerase beta.
NMR assignments of the full-length protein (335 residues, 39 kDa) in the presence of a double gap--double hairpin DNA (22 nucleotides, 7 kDa)
Title: NMR assignment of polymerase beta labeled with 2H, 13C, and 15N in complex with substrate DNA.
for Pol beta, fidelity is dictated by the differences in free energy required to reach the highest energy transition state of the chemical step.
Title: Contribution of the reverse rate of the conformational step to polymerase beta fidelity.
Loop II of pol beta functions to maintain accurate DNA synthesis by a direct or indirect influence on the nucleotide binding pocket.
Title: Loop II of DNA polymerase beta is important for discrimination during substrate binding.
Changes in the activity and expression of DNA polymerase beta are mediated via cAMP and the A-kinase system, and that phosphorylation of this enzyme is also involved in this expression.
Title: Hormonal regulation of DNA polymerase beta activity and expression in rat adrenal glands and testes.

Submit: New GeneRIF Correction See all GeneRIFs (22)

General gene information

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Markers

D8S2287 (e-PCR)
- UniSTS:473963

D8S2288 (e-PCR)
- UniSTS:473964

RH130718 (e-PCR)
- UniSTS:214002

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 5'-deoxyribose-5-phosphate lyase activity	ISO Inferred from Sequence Orthology more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-directed DNA polymerase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-directed DNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-directed DNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables DNA-directed DNA polymerase activity	ISO Inferred from Sequence Orthology more info
enables DNA-directed DNA polymerase activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-directed DNA polymerase activity	TAS Traceable Author Statement more info	PubMed
enables class I DNA-(apurinic or apyrimidinic site) endonuclease activity	ISO Inferred from Sequence Orthology more info
enables damaged DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables lyase activity	IEA Inferred from Electronic Annotation more info
enables lyase activity	ISO Inferred from Sequence Orthology more info
enables lyase activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables microtubule binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA damage response	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in base-excision repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in base-excision repair	ISO Inferred from Sequence Orthology more info
involved_in base-excision repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in base-excision repair	TAS Traceable Author Statement more info	PubMed
involved_in base-excision repair, gap-filling	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within base-excision repair, gap-filling	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via nonhomologous end joining	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within homeostasis of number of cells	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within immunoglobulin heavy chain V-D-J recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inflammatory response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lymph node development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron apoptotic process	ISO Inferred from Sequence Orthology more info
NOT involved_in nucleotide-excision repair, DNA gap filling	ISO Inferred from Sequence Orthology more info
involved_in pyrimidine dimer repair	IDA Inferred from Direct Assay more info	PubMed
involved_in response to ethanol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to gamma radiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hyperoxia	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within salivary gland morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic diversification of immunoglobulins	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic hypermutation of immunoglobulin genes	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spleen development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in microtubule	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
located_in spindle microtubule	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA polymerase beta

Names: 5'-dRP lyase; 5'-deoxyribose-phosphate lyase; AP lyase; DNA pol beta; DNA-directed DNA polymerase beta; polymerase (DNA directed), beta; polymerase (DNA) beta; polymerase-beta

NP_058837.2

EC 2.7.7.7

EC 4.2.99.18

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.