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Protein

DNA polymerase beta

Gene

polb

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases (By similarity).By similarity

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactori

Mg2+By similarityNote: Binds 2 magnesium ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei72Schiff-base intermediate with DNABy similarity1
Metal bindingi101Sodium; via carbonyl oxygenBy similarity1
Metal bindingi103Sodium; via carbonyl oxygenBy similarity1
Metal bindingi106Sodium; via carbonyl oxygenBy similarity1
Metal bindingi190Magnesium 1By similarity1
Metal bindingi190Magnesium 2By similarity1
Metal bindingi192Magnesium 1By similarity1
Metal bindingi192Magnesium 2By similarity1
Metal bindingi255Magnesium 2By similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, DNA-directed DNA polymerase, Lyase, Nucleotidyltransferase, Transferase
Biological processDNA damage, DNA repair, DNA replication, DNA synthesis
LigandMagnesium, Metal-binding, Sodium

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase beta (EC:2.7.7.7, EC:4.2.99.-)
Gene namesi
Name:polb
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-999702 polb

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002187822 – 334DNA polymerase betaAdd BLAST333

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei83Omega-N-methylarginine; by PRMT6By similarity1
Modified residuei152Omega-N-methylarginine; by PRMT6By similarity1

Post-translational modificationi

Methylation by PRMT6 stimulates the polymerase activity by enhancing DNA binding and processivity.By similarity
Ubiquitinated: monoubiquitinated by huwe1/arf-bp1. Monoubiquitinated protein is then the target of stub1/chip, which catalyzes polyubiquitination from monoubiquitin, leading to degradation by the proteasome. usp47 mediates the deubiquitination of monoubiquitinated protein, preventing polyubiquitination by STUB1/CHIP and its subsequent degradation (By similarity).By similarity

Keywords - PTMi

Methylation, Ubl conjugation

Proteomic databases

MaxQBiO57383

Interactioni

Subunit structurei

Monomer.

Structurei

3D structure databases

ProteinModelPortaliO57383
SMRiO57383
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni183 – 192DNA bindingBy similarity10

Sequence similaritiesi

Belongs to the DNA polymerase type-X family.Curated

Phylogenomic databases

HOVERGENiHBG002359
KOiK02330

Family and domain databases

CDDicd00141 NT_POLXc, 1 hit
Gene3Di1.10.150.110, 1 hit
3.30.210.10, 1 hit
InterProiView protein in InterPro
IPR002054 DNA-dir_DNA_pol_X
IPR019843 DNA_pol-X_BS
IPR010996 DNA_pol_b-like_N
IPR028207 DNA_pol_B_palm_palm
IPR018944 DNA_pol_lambd_fingers_domain
IPR027421 DNA_pol_lamdba_lyase_dom_sf
IPR037160 DNA_Pol_thumb_sf
IPR022312 DNA_pol_X
IPR002008 DNA_pol_X_beta-like
IPR003583 Hlx-hairpin-Hlx_DNA-bd_motif
IPR029398 PolB_thumb
PfamiView protein in Pfam
PF14792 DNA_pol_B_palm, 1 hit
PF14791 DNA_pol_B_thumb, 1 hit
PF10391 DNA_pol_lambd_f, 1 hit
PF14716 HHH_8, 1 hit
PRINTSiPR00869 DNAPOLX
PR00870 DNAPOLXBETA
SMARTiView protein in SMART
SM00278 HhH1, 2 hits
SM00483 POLXc, 1 hit
SUPFAMiSSF47802 SSF47802, 1 hit
PROSITEiView protein in PROSITE
PS00522 DNA_POLYMERASE_X, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O57383-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKRKAPQES PNEGITDFLV ELANYERNVN RAIHKYNAYR KAASVIAKYP
60 70 80 90 100
TKIKSGTEAK KLDGVGAKIA EKIDEFLATG KLRKLEKIRQ DDTSSSINFL
110 120 130 140 150
TRVTGIGPAA ARKFFDEGIK TLDDLRNNEH KLNHHQKIGL KHFDDFEKRI
160 170 180 190 200
PRKEMLQMQE IILDKVNNLD PEYIATVCGS FRRGAESSGD MDILLTHPDF
210 220 230 240 250
TSESAKQPRL LHQVVQCLED CNFITDTLVK GDTKFMGVCQ LPCESDQDYP
260 270 280 290 300
YRRIDIRLIP KDQYYCGVLY FTGSDIFNKN MRTHALEKGF TLNEYTLRPL
310 320 330
GVTGIAGEPL PIDSEKDIFD YIQWKYREPK DRSE
Length:334
Mass (Da):38,294
Last modified:January 23, 2007 - v3
Checksum:i33073FF0D0554458
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y15732 mRNA Translation: CAA75741.1
BC106329 mRNA Translation: AAI06330.1
RefSeqiNP_001081643.1, NM_001088174.1
UniGeneiXl.56

Genome annotation databases

GeneIDi397973
KEGGixla:397973

Similar proteinsi

Entry informationi

Entry nameiDPOLB_XENLA
AccessioniPrimary (citable) accession number: O57383
Secondary accession number(s): Q3KQ91
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 23, 2007
Last modified: November 22, 2017
This is version 105 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health