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Protein

DNA polymerase beta

Gene

Polb

Organism
Rattus norvegicus (Rat)
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.

Catalytic activityi

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

Cofactori

Mg2+Note: Binds 2 magnesium ions per subunit.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei72Schiff-base intermediate with DNABy similarity1
Metal bindingi101Sodium; via carbonyl oxygen1
Metal bindingi103Sodium; via carbonyl oxygen1
Metal bindingi106Sodium; via carbonyl oxygen1
Metal bindingi190Magnesium 11
Metal bindingi190Magnesium 21
Metal bindingi192Magnesium 11
Metal bindingi192Magnesium 21
Metal bindingi256Magnesium 21

GO - Molecular functioni

  • damaged DNA binding Source: RGD
  • DNA binding Source: UniProtKB
  • DNA-directed DNA polymerase activity Source: RGD
  • enzyme binding Source: Ensembl
  • lyase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB
  • microtubule binding Source: Ensembl

GO - Biological processi

  • aging Source: RGD
  • base-excision repair Source: UniProtKB
  • base-excision repair, gap-filling Source: RGD
  • cellular response to DNA damage stimulus Source: UniProtKB
  • DNA biosynthetic process Source: RGD
  • DNA replication Source: UniProtKB-KW
  • homeostasis of number of cells Source: Ensembl
  • immunoglobulin heavy chain V-D-J recombination Source: Ensembl
  • inflammatory response Source: Ensembl
  • intrinsic apoptotic signaling pathway in response to DNA damage Source: Ensembl
  • lymph node development Source: Ensembl
  • neuron apoptotic process Source: Ensembl
  • pyrimidine dimer repair Source: RGD
  • response to ethanol Source: RGD
  • response to gamma radiation Source: RGD
  • response to hyperoxia Source: RGD
  • salivary gland morphogenesis Source: Ensembl
  • somatic hypermutation of immunoglobulin genes Source: Ensembl
  • spleen development Source: Ensembl

Keywordsi

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

Enzyme and pathway databases

ReactomeiR-RNO-110362 POLB-Dependent Long Patch Base Excision Repair
R-RNO-110373 Resolution of AP sites via the multiple-nucleotide patch replacement pathway
R-RNO-110381 Resolution of AP sites via the single-nucleotide replacement pathway
R-RNO-5649702 APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway
R-RNO-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-RNO-5689880 Ub-specific processing proteases
R-RNO-73930 Abasic sugar-phosphate removal via the single-nucleotide replacement pathway

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase beta (EC:2.7.7.7, EC:4.2.99.-)
Gene namesi
Name:Polb
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 16

Organism-specific databases

RGDi3363 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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi190D → E or S: Loss of activity. 1 Publication1
Mutagenesisi191M → I: No loss of activity. 1
Mutagenesisi191M → T: 50% loss of activity. 1
Mutagenesisi192D → E or S: Loss of activity. 1 Publication1
Mutagenesisi246D → V: Misincorporates T nucleotide opposite G/C template. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL4343

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002187801 – 335DNA polymerase betaAdd BLAST335

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki41Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei72N6-acetyllysineBy similarity1
Cross-linki81Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
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 at Lys-41, Lys-61 and Lys-81: 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

Acetylation, Isopeptide bond, Methylation, Ubl conjugation

Proteomic databases

PaxDbiP06766
PRIDEiP06766

PTM databases

iPTMnetiP06766
PhosphoSitePlusiP06766

Expressioni

Gene expression databases

BgeeiENSRNOG00000019150
GenevisibleiP06766 RN

Interactioni

Subunit structurei

Interacts with APEX1, HUWE1/ARF-BP1, STUB1/CHIP and USP47 (By similarity). Monomer. Interacts with FAM168A (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
XRCC1P188874EBI-15845002,EBI-947466From Homo sapiens.

GO - Molecular functioni

Protein-protein interaction databases

DIPiDIP-44707N
IntActiP06766, 1 interactor
STRINGi10116.ENSRNOP00000026039

Chemistry databases

BindingDBiP06766

Structurei

Secondary structure

1335
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi13 – 28Combined sources16
Beta strandi29 – 31Combined sources3
Helixi33 – 48Combined sources16
Helixi56 – 61Combined sources6
Beta strandi62 – 64Combined sources3
Helixi67 – 76Combined sources10
Beta strandi79 – 81Combined sources3
Helixi83 – 90Combined sources8
Helixi92 – 100Combined sources9
Turni101 – 104Combined sources4
Helixi108 – 115Combined sources8
Turni116 – 118Combined sources3
Helixi122 – 126Combined sources5
Helixi129 – 131Combined sources3
Helixi134 – 141Combined sources8
Turni142 – 144Combined sources3
Helixi145 – 147Combined sources3
Helixi152 – 169Combined sources18
Beta strandi174 – 177Combined sources4
Helixi179 – 182Combined sources4
Beta strandi186 – 196Combined sources11
Turni202 – 204Combined sources3
Helixi208 – 220Combined sources13
Beta strandi224 – 230Combined sources7
Beta strandi232 – 239Combined sources8
Beta strandi244 – 247Combined sources4
Beta strandi253 – 259Combined sources7
Helixi262 – 264Combined sources3
Helixi265 – 273Combined sources9
Helixi276 – 288Combined sources13
Beta strandi291 – 293Combined sources3
Beta strandi298 – 301Combined sources4
Beta strandi303 – 305Combined sources3
Helixi316 – 322Combined sources7
Helixi330 – 332Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BNONMR-A1-87[»]
1BNPNMR-A1-87[»]
1BPBX-ray2.30A88-335[»]
1BPDX-ray3.60A1-335[»]
1BPEX-ray2.90A1-335[»]
1DK2NMR-A2-87[»]
1DK3NMR-A1-87[»]
1HUOX-ray2.60A/B1-335[»]
1HUZX-ray2.60A/B1-335[»]
1JN3X-ray2.35A85-335[»]
1NOMX-ray3.00A88-335[»]
1RPLX-ray2.30A85-335[»]
1ZQUX-ray2.60A88-335[»]
1ZQVX-ray2.70A88-335[»]
1ZQWX-ray2.30A88-335[»]
1ZQXX-ray2.50A88-335[»]
1ZQYX-ray2.30A88-335[»]
1ZQZX-ray2.70A88-335[»]
2BPCX-ray2.80A88-335[»]
2BPFX-ray2.90A1-335[»]
2BPGX-ray3.60A/B1-335[»]
2VANX-ray2.10A91-335[»]
3K75X-ray2.95D/E91-335[»]
3LQCX-ray2.35B142-335[»]
3UXNX-ray2.50A/B1-335[»]
3UXOX-ray2.10A/B1-335[»]
3UXPX-ray2.72A/B1-335[»]
3V72X-ray2.49A1-335[»]
3V7JX-ray2.25A4-335[»]
3V7KX-ray2.27A4-335[»]
3V7LX-ray2.66A4-335[»]
ProteinModelPortaliP06766
SMRiP06766
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06766

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni183 – 192DNA binding10

Domaini

Residues 239-252 form a flexible loop which appears to affect the polymerase fidelity.

Sequence similaritiesi

Belongs to the DNA polymerase type-X family.Curated

Phylogenomic databases

eggNOGiKOG2534 Eukaryota
COG1796 LUCA
GeneTreeiENSGT00530000063002
HOGENOMiHOG000007787
HOVERGENiHBG002359
InParanoidiP06766
KOiK02330
OMAiDLFNKNM
OrthoDBiEOG091G0HMG
PhylomeDBiP06766
TreeFamiTF103002

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.

P06766-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKRKAPQET LNGGITDMLV ELANFEKNVS QAIHKYNAYR KAASVIAKYP
60 70 80 90 100
HKIKSGAEAK KLPGVGTKIA EKIDEFLATG KLRKLEKIRQ DDTSSSINFL
110 120 130 140 150
TRVTGIGPSA ARKLVDEGIK TLEDLRKNED KLNHHQRIGL KYFEDFEKRI
160 170 180 190 200
PREEMLQMQD IVLNEVKKLD PEYIATVCGS FRRGAESSGD MDVLLTHPNF
210 220 230 240 250
TSESSKQPKL LHRVVEQLQK VRFITDTLSK GETKFMGVCQ LPSENDENEY
260 270 280 290 300
PHRRIDIRLI PKDQYYCGVL YFTGSDIFNK NMRAHALEKG FTINEYTIRP
310 320 330
LGVTGVAGEP LPVDSEQDIF DYIQWRYREP KDRSE
Length:335
Mass (Da):38,327
Last modified:January 23, 2007 - v4
Checksum:iBBF8498C0D3FBFC9
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti228L → R in AAA41901 (PubMed:3597402).Curated1
Sequence conflicti228L → R in AAB00389 (Ref. 2) Curated1
Sequence conflicti228L → R in AAA41900 (PubMed:2873575).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02776 mRNA Translation: AAA41901.1
U38801 mRNA Translation: AAB00389.1
BC098668 mRNA Translation: AAH98668.1
M13961 mRNA Translation: AAA41900.1
PIRiA27112
RefSeqiNP_058837.2, NM_017141.2
UniGeneiRn.9346

Genome annotation databases

EnsembliENSRNOT00000026039; ENSRNOP00000026039; ENSRNOG00000019150
GeneIDi29240
KEGGirno:29240
UCSCiRGD:3363 rat

Similar proteinsi

Entry informationi

Entry nameiDPOLB_RAT
AccessioniPrimary (citable) accession number: P06766
Secondary accession number(s): Q4G081
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 184 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health