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Protein

DNA polymerase

Gene

2

Organism
Bacillus phage phi29 (Bacteriophage phi-29)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Polymerase responsible for protein-primed viral DNA replication by strand displacement with high processivity and fidelity (PubMed:3863101) (PubMed:2498321). To start replication, the DNA polymerase forms a heterodimer with a free primer terminal protein (TP), recognizes the replication origins at both 5' ends of the linear chromosome, and initiates replication using as primer the OH-group of Ser-232 of the TP (PubMed:22210885). This polymerase possesses three enzymatic activities: DNA synthesis (polymerase), primer terminal protein (TP) deoxynucleotidylation, which is the formation of a covalent linkage (phosphoester) between the hydroxyl group of a specific serine residue in TP and 5'-dAMP, a reaction directed by the second T at the 3' end, and 3' to 5' exonuclease activity (PubMed:2790959). Exonuclease activity has a proofreading purpose (PubMed:2790959). DNA polymerase edits the polymerization errors using an intramolecular pathway as the primer terminus travels from one active site to the other without dissociation from the DNA (PubMed:10493855). DNA polymerization catalyzed by the DNA polymerase is a highly accurate process, but the protein-primed initiation is a quite inaccurate reaction (PubMed:8428945). Since the polymerase initiates the replication on the second thymine, the TP-dAMP initiation product translocates backwards to recover the template information of the first nucleotide (sliding back-mechanism) (PubMed:19011105).9 Publications

Catalytic activityi

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

Cofactori

Mg2+4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei12Essential for 3'-5' exonucleolysis2 Publications1
Sitei14Essential for 3'-5' exonucleolysis2 Publications1
Sitei15Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site1 Publication1
Sitei62Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site1 Publication1
Sitei65Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei66Essential for 3'-5' exonucleolysis2 Publications1
Sitei93Involved in binding template-primer structures1 Publication1
Sitei122Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei123Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Metal bindingi145Magnesium 1Combined sources1
Sitei148Involved in the stabilization of the frayed 3' terminus at the exonuclease active site1 Publication1
Metal bindingi169Magnesium 1Combined sources1
Metal bindingi249Magnesium 2; catalyticCombined sources1 Publication1
Metal bindingi250Magnesium 2; via carbonyl oxygen; catalyticCombined sources1 Publication1
Sitei252Probably involved in binding template-primer structures1 Publication1
Binding sitei254TTP; via amide nitrogenCombined sources1
Sitei254Probably involved in nucleotide binding selection1 Publication1
Sitei356Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei364Involved in the binding of DNA and dNTP1 Publication1
Sitei366Stabilization of the incoming nucleotide1 Publication1
Binding sitei371TTPCombined sources1
Sitei371Interacts with the phosphate groups of the incoming nucleotide1 Publication1
Sitei379Stabilization of the incoming nucleotide1 Publication1
Binding sitei383TTPCombined sources1
Sitei383Probably involved in nucleotide binding selection1 Publication1
Sitei384Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity1 Publication1
Sitei387Probably involved in binding template-primer structures1 Publication1
Sitei390Probably involved in nucleotide binding selection1 Publication1
Sitei391Probably involved in binding template-primer structures1 Publication1
Sitei420Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication1
Sitei434Probably involved in binding template-primer structures1 Publication1
Sitei438Probably involved in binding template-primer structures1 Publication1
Metal bindingi456Magnesium 2; catalytic1 Publication1
Metal bindingi458Magnesium 2; catalyticCombined sources1
Binding sitei458TTPCombined sources1
Sitei498Probably involved in binding template-primer structures1 Publication1
Sitei500Probably involved in binding template-primer structures1 Publication1
Sitei529Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities1 Publication1

GO - Molecular functioni

GO - Biological processi

  • viral DNA genome replication Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Viral DNA replication

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase (EC:2.7.7.71 Publication, EC:3.1.11.-1 Publication)
Alternative name(s):
Gene product 2Curated
Short name:
gp2Curated
Protein p2Curated
Gene namesi
Name:2
OrganismiBacillus phage phi29 (Bacteriophage phi-29)
Taxonomic identifieri10756 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesPodoviridaePicovirinaePhi29likevirus
Virus hostiBacillus subtilis [TaxID: 1423]
Proteomesi
  • UP000001207 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi12D → A: Strong loss of 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi14E → A: Strong loss of 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi15T → I: 95% loss of ssDNA-binding. Decreased in fidelity of DNA replication. 1 Publication1
Mutagenesisi59Y → F: Almost no effect on replication activity. About 20% loss of TP-DNA initiation, 20% loss of TP-DNA replication and 10% loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi59Y → L: 3 fold decrease in replication activity. About 80% loss of TP-DNA initiation, 70% loss of TP-DNA replication and 97% loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi59Y → R: 3 fold decrease in replication activity. About 75% loss of TP-DNA initiation, complete loss of TP-DNA replication and complete loss of TP-DNA amplification. 1 Publication1
Mutagenesisi61H → L: 5 fold decrease in replication activity. About 85% loss of TP-DNA initiation, 80% loss of TP-DNA replication and complete loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi61H → R: 100 fold decrease in replication activity. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi62N → D or H: 88% loss of ssDNA-binding. Decreased in fidelity of DNA replication. 1 Publication1
Mutagenesisi65F → S: Loss of capacity to interact with a DNA primer/template structure. 1 Publication1
Mutagenesisi66D → A: Strong loss of 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi69F → S: 2 fold decrease in replication activity. About 50% loss of TP-DNA initiation, 40% loss of TP-DNA replication and 60% loss of TP-DNA amplification. Complete loss of interaction with TP. 1 Publication1
Mutagenesisi69F → Y: 2 fold decrease in replication activity. About 80% loss of TP-DNA initiation, 50% loss of TP-DNA replication and almost 95% loss of TP-DNA. Complete loss of interaction with TP amplification. 1 Publication1
Mutagenesisi122S → T: Loss of capacity to interact with a DNA primer/template structure. 1 Publication1
Mutagenesisi123L → N: Loss of capacity to interact with a DNA primer/template structure. 1 Publication1
Mutagenesisi128F → A: Slight loss of interaction with TP. 1 Publication1
Mutagenesisi128F → Y: Almost complete loss of interaction with TP. 1 Publication1
Mutagenesisi143K → I or R: Strong loss of 3'-5' exonuclease, proofreading and strand-displacement activities. 1 Publication1
Mutagenesisi148Y → A: Reduced capacity to stabilize the binding of the primer terminus at the 3'-5' exonuclease active site. 1 Publication1
Mutagenesisi169D → A: Strong loss of 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi187R → K: No effect on DNA-binding, TP binding and replication/amplification. 1 Publication1
Mutagenesisi189T → A: No effect on DNA-binding, TP binding and replication/amplification. 1 Publication1
Mutagenesisi192S → I: Loss of DNA-binding. Reduced TP binding. 25% loss of replication and almost complete loss of amplification. 1 Publication1
Mutagenesisi192S → N: Loss of DNA-binding. No effect on TP binding. 50% loss of replication/amplification. 1 Publication1
Mutagenesisi196K → I: Loss of DNA-binding. Reduced TP binding. 25% loss of replication and almost complete loss of amplification. 6-fold reduced 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi196K → R: Slight loss of DNA-binding. No loss of replication and amplification. 1 Publication1
Mutagenesisi198F → V: Loss of DNA-binding. Reduced TP binding. 25% loss of replication and almost complete loss of amplification. 6-fold reduced 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi206K → I: No effect on DNA-binding. Reduced TP binding. 70% loss of replication and 20% loss of amplification. 1 Publication1
Mutagenesisi223R → I: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi226Y → F: Favored polymerization (high pol/exo ratio). decrease in forward and reverse rates of translocation. Increased affinity for dNTP and for pyrophosphate in the pre-translocation state. 3 Publications1
Mutagenesisi226Y → S: Favored exonucleolysis. Complete loss of polymerization. 2 Publications1
Mutagenesisi227R → I: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi227R → K: No effect on the pol/exo ratio. 1 Publication1
Mutagenesisi228G → A: Favored polymerization (high pol/exo ratio). 2 Publications1
Mutagenesisi229G → A: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi229G → D: Favored exonucleolysis. Complete loss of polymerization. 2 Publications1
Mutagenesisi230F → A: Favored polymerization (high pol/exo ratio). 2 Publications1
Mutagenesisi230F → S: Favored exonucleolysis (low pol/exo ratio). 2 Publications1
Mutagenesisi230F → Y: No effect on the pol/exo ratio. 1 Publication1
Mutagenesisi249D → E: Complete loss of DNA polymerase activity. Slight decrease in template-primer binding. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi250V → A: No effect on TP-DNA replication. 1 Publication1
Mutagenesisi250V → F: Complete loss of TP-DNA replication. 1 Publication1
Mutagenesisi251N → D: No effect on TP-DNA replication. 1 Publication1
Mutagenesisi252S → G: 40% loss of DNA polymerase activity. No effect on translocation or stabilization of the incorporated nucIeotide. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi252S → R: Complete loss of DNA polymerase activity. Drastic loss of template-primer binding. No effect on 3' to 5' exonucleolysis and interaction with the TP primer. 1 Publication1
Mutagenesisi253L → V: 30% loss of DNA polymerase activity. No effect on translocation or stabilization of the incorporated nucIeotide. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi254Y → F: Decreased dNTP binding affinity. 10-fold reduced affinity for the correct nucleotide. 1 Publication1
Mutagenesisi254Y → V: Loss of discrimination for rNTPs over dNTPs. 1 Publication1
Mutagenesisi255P → S: 30% loss of DNA polymerase activity. No effect on translocation or stabilization of the incorporated nucIeotide. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi364I → Q: Partial loss of hability to stably bind the DNA substrate. 1 Publication1
Mutagenesisi364I → R: Complete loss of hability to stably bind the DNA substrate. 1 Publication1
Mutagenesisi366K → T: Slight decrease in DNA-binding capacity. No effect on polymerisation activity, except that it is reduced in the absence of a DNA template. Reduced affinity for the initiating nucleotide. 3 fold reduction of the initiation activity in the presence of p6. 1 Publication1
Mutagenesisi371K → T: Strong decrease in the affinity for dNTPs and pyrophosphorolytic activity. No effect on exonucleolysis. 1 Publication1
Mutagenesisi379K → T: Slight increase in DNA-binding capacity. Reduced affinity for the initiating nucleotide. 1 Publication1
Mutagenesisi383K → P: Complete loss of incorporation of dNTP substrates using either DNA or TP as primer. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi383K → R: Strong loss of ability to use dNTPs in both processive and non-processive DNA synthesis. Impaired progression from protein-primed initiation to DNA elongation. No effect on 3' to 5' exonucleolysis. 1 Publication1
Mutagenesisi384L → R: Reduced nucleotide insertion fidelity during DNA-primed polymerization and protein-primed initiation. No effect on the affinity for the different dNTPs. 1 Publication1
Mutagenesisi387N → Y: 3-fold higher Km value for dATP and more than 11-fold lower Vmax value than the wild-type enzyme in the initiation reaction. Impaired in enzyme-DNA translocation. 1 Publication1
Mutagenesisi388S → G: No effect on initiation and polymerization activities. Increased efficiency of dNTP incorporation in non-templated reactions. 1 Publication1
Mutagenesisi390Y → F: Decreased dNTP binding affinity in the post-translocation state. 4.6-fold reduced affinity for the correct nucleotide. 2 Publications1
Mutagenesisi390Y → S: Decreased dNTP binding affinity. 14-fold reduced affinity for the correct nucleotide. Loss of discrimination against dA insertion opposite 8oxodG. 2 Publications1
Mutagenesisi391G → D: Complete loss of template-primer binding. 1 Publication1
Mutagenesisi392K → Q: 50% loss of exonuclease activity. 80% loss of processivity. No effect on DNA polymerase/DNA complex formation. 1 Publication1
Mutagenesisi392K → R: 90% loss of exonuclease activity. 80% loss of processivity. No effect on DNA polymerase/DNA complex formation. 1 Publication1
Mutagenesisi393F → Y: Severe decrease in initial binding to template-primer DNA molecules. 1 Publication1
Mutagenesisi434T → N: Complete loss of TP-dAMP formation. Almost complete loss of DNA polymerization. 1 Publication1
Mutagenesisi437A → G: No effect on TP-dAMP formation. 20% loss of DNA polymerization. 1 Publication1
Mutagenesisi438R → I: Complete loss of TP-dAMP formation. Almost complete loss of DNA polymerization. 1 Publication1
Mutagenesisi438R → K: Complete loss of TP-dAMP formation. 30% loss of DNA polymerization. 1 Publication1
Mutagenesisi454Y → F: No effect on the formation of the covalent complex between the TP and 5'-dAMP. Loss of replication of a p3-DNA complex or a primed M13 DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi455C → G: 65% loss of formation of the covalent complex between the TP and 5'-dAMP. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi456D → G: 50% loss of synthetic activities, TP-primed initiation and DNA-primed polymerization. When polymerization requires an efficient translocation along the template, catalytic efficiency is strongly reduced. 90% loss of formation of the covalent complex between the TP and 5'-dAMP. Increased 3'-5' exonucleolysis. 2 Publications1
Mutagenesisi457T → P: Complete loss of initiation and polymerization activities. Severe loss of protein-priming activity. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi458D → G: Complete loss of initiation and polymerization activities. Severe loss of protein-priming activity. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi498K → R: Strong decrease in DNA polymerization activity. Loss of binding to a primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi498K → T: Strong decrease in initiation and DNA polymerization activities. Loss of binding to a primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi500Y → S: Strong decrease in DNA polymerization activity and interaction with primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication1
Mutagenesisi529K → A: Increased exonuclease activity and loss of primer elongation. Deficient in nucleotide incorporation. 1 Publication1
Mutagenesisi529K → E: Increased exonuclease activity and complete loss of primer elongation. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000465421 – 575DNA polymeraseAdd BLAST575

Expressioni

Keywords - Developmental stagei

Early protein

Interactioni

Subunit structurei

Interacts with the primer terminal protein; this interaction allows the initiation of TP-primed DNA replication at both viral DNA ends. Interacts with DNA.3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei59Interaction with the primer terminal protein1 Publication1
Sitei61Interaction with the primer terminal protein1 Publication1
Sitei69Interaction with the primer terminal protein1 Publication1

Structurei

Secondary structure

1575
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 15Combined sources8
Beta strandi19 – 21Combined sources3
Beta strandi24 – 33Combined sources10
Beta strandi38 – 42Combined sources5
Helixi44 – 54Combined sources11
Beta strandi57 – 62Combined sources6
Helixi63 – 76Combined sources14
Beta strandi89 – 95Combined sources7
Beta strandi100 – 110Combined sources11
Beta strandi113 – 121Combined sources9
Helixi122 – 125Combined sources4
Helixi130 – 136Combined sources7
Beta strandi148 – 150Combined sources3
Helixi160 – 182Combined sources23
Beta strandi187 – 189Combined sources3
Helixi190 – 202Combined sources13
Helixi204 – 210Combined sources7
Helixi216 – 223Combined sources8
Beta strandi231 – 233Combined sources3
Helixi235 – 237Combined sources3
Beta strandi238 – 242Combined sources5
Beta strandi244 – 250Combined sources7
Helixi253 – 260Combined sources8
Beta strandi263 – 274Combined sources12
Beta strandi283 – 294Combined sources12
Beta strandi308 – 310Combined sources3
Beta strandi324 – 329Combined sources6
Helixi330 – 339Combined sources10
Beta strandi340 – 357Combined sources18
Helixi361 – 373Combined sources13
Helixi376 – 387Combined sources12
Helixi390 – 393Combined sources4
Beta strandi401 – 406Combined sources6
Beta strandi410 – 416Combined sources7
Helixi427 – 447Combined sources21
Turni448 – 451Combined sources4
Beta strandi452 – 456Combined sources5
Beta strandi459 – 466Combined sources8
Helixi469 – 474Combined sources6
Beta strandi477 – 479Combined sources3
Beta strandi482 – 496Combined sources15
Beta strandi499 – 509Combined sources11
Beta strandi512 – 515Combined sources4
Beta strandi518 – 520Combined sources3
Beta strandi522 – 530Combined sources9
Helixi535 – 538Combined sources4
Turni543 – 545Combined sources3
Beta strandi551 – 561Combined sources11
Beta strandi564 – 573Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1XHXX-ray2.35A/B/C/D1-575[»]
1XHZX-ray2.70A/B/C/D1-575[»]
1XI1X-ray2.20A/B1-575[»]
2EX3X-ray3.00A/C/E/G/I/K1-575[»]
2PY5X-ray1.60A/B1-575[»]
2PYJX-ray2.03A/B1-575[»]
2PYLX-ray2.20A1-575[»]
2PZSX-ray2.60A/B/C/D1-575[»]
ProteinModelPortaliP03680.
SMRiP03680.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03680.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 1913'-5' exonuclease and strand displacement activities1 PublicationAdd BLAST191
Regioni192 – 229Involved in DNA-binding, coordination between DNA synthesis and degradation and TP interaction3 PublicationsAdd BLAST38
Regioni230 – 562Initiation, polymerization and pyrophosphorolytic activities1 PublicationAdd BLAST333
Regioni398 – 420TPR21 PublicationAdd BLAST23
Regioni563 – 575Involved in DNA-binding and TP interaction1 PublicationAdd BLAST13

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi454 – 458YCDTD1 Publication5

Domaini

The N-terminus contains the 3'-5' exonuclease activity and strand displacement ability (PubMed:8621470). The conserved motif YxGG/A located between the 3'-5' exonuclease and polymerization domains is important for DNA-binding, coordination between DNA synthesis and degradation and for the formation of a stable complex between TP and the DNA polymerase (PubMed:8670845, PubMed:9931249, PubMed:15777661). The C-terminus is involved in the protein-primed initiation, DNA polymerization and pyrophosphorolytic activities (PubMed:8621470, PubMed:1850426). The YCDTD motif is essential for the pyrophosphorolytic activity (PubMed:1850426). The TPR2 region is necessary for the strand displacement coupled to DNA synthesis and probably also for allowing the TP priming domain to move out from the polymerase during transition from initiation to elongation (PubMed:15845765, PubMed:19033368).6 Publications

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
InterProiIPR006172. DNA-dir_DNA_pol_B.
IPR017964. DNA-dir_DNA_pol_B_CS.
IPR004868. DNA-dir_DNA_pol_B_mt/vir.
IPR014416. DNA-dir_DNA_polB_phi29_vir.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF03175. DNA_pol_B_2. 1 hit.
[Graphical view]
PIRSFiPIRSF004178. Dpol_Bac_phage. 1 hit.
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P03680-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKHMPRKMYS CDFETTTKVE DCRVWAYGYM NIEDHSEYKI GNSLDEFMAW
60 70 80 90 100
VLKVQADLYF HNLKFDGAFI INWLERNGFK WSADGLPNTY NTIISRMGQW
110 120 130 140 150
YMIDICLGYK GKRKIHTVIY DSLKKLPFPV KKIAKDFKLT VLKGDIDYHK
160 170 180 190 200
ERPVGYKITP EEYAYIKNDI QIIAEALLIQ FKQGLDRMTA GSDSLKGFKD
210 220 230 240 250
IITTKKFKKV FPTLSLGLDK EVRYAYRGGF TWLNDRFKEK EIGEGMVFDV
260 270 280 290 300
NSLYPAQMYS RLLPYGEPIV FEGKYVWDED YPLHIQHIRC EFELKEGYIP
310 320 330 340 350
TIQIKRSRFY KGNEYLKSSG GEIADLWLSN VDLELMKEHY DLYNVEYISG
360 370 380 390 400
LKFKATTGLF KDFIDKWTYI KTTSEGAIKQ LAKLMLNSLY GKFASNPDVT
410 420 430 440 450
GKVPYLKENG ALGFRLGEEE TKDPVYTPMG VFITAWARYT TITAAQACYD
460 470 480 490 500
RIIYCDTDSI HLTGTEIPDV IKDIVDPKKL GYWAHESTFK RAKYLRQKTY
510 520 530 540 550
IQDIYMKEVD GKLVEGSPDD YTDIKFSVKC AGMTDKIKKE VTFENFKVGF
560 570
SRKMKPKPVQ VPGGVVLVDD TFTIK
Length:575
Mass (Da):66,714
Last modified:July 21, 1986 - v1
Checksum:i856EEB6B04A7E268
GO

Sequence cautioni

The sequence ACE96023 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti492A → V in CAA37450 (PubMed:2118623).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti176A → R in mutant TS2(24). 1
Natural varianti355A → V in mutant TS2(24). 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01155 Genomic DNA. Translation: CAA24480.1.
X53370 Genomic DNA. Translation: CAA37450.1.
EU771092 Genomic DNA. Translation: ACE96023.1. Different initiation.
X53371 Genomic DNA. Translation: CAA37451.1.
PIRiA04282. ERBP29.
RefSeqiYP_002004529.1. NC_011048.1.

Genome annotation databases

GeneIDi6446511.
KEGGivg:6446511.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01155 Genomic DNA. Translation: CAA24480.1.
X53370 Genomic DNA. Translation: CAA37450.1.
EU771092 Genomic DNA. Translation: ACE96023.1. Different initiation.
X53371 Genomic DNA. Translation: CAA37451.1.
PIRiA04282. ERBP29.
RefSeqiYP_002004529.1. NC_011048.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1XHXX-ray2.35A/B/C/D1-575[»]
1XHZX-ray2.70A/B/C/D1-575[»]
1XI1X-ray2.20A/B1-575[»]
2EX3X-ray3.00A/C/E/G/I/K1-575[»]
2PY5X-ray1.60A/B1-575[»]
2PYJX-ray2.03A/B1-575[»]
2PYLX-ray2.20A1-575[»]
2PZSX-ray2.60A/B/C/D1-575[»]
ProteinModelPortaliP03680.
SMRiP03680.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi6446511.
KEGGivg:6446511.

Miscellaneous databases

EvolutionaryTraceiP03680.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
InterProiIPR006172. DNA-dir_DNA_pol_B.
IPR017964. DNA-dir_DNA_pol_B_CS.
IPR004868. DNA-dir_DNA_pol_B_mt/vir.
IPR014416. DNA-dir_DNA_polB_phi29_vir.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF03175. DNA_pol_B_2. 1 hit.
[Graphical view]
PIRSFiPIRSF004178. Dpol_Bac_phage. 1 hit.
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPOL_BPPH2
AccessioniPrimary (citable) accession number: P03680
Secondary accession number(s): B3VMN6, Q38545
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: November 2, 2016
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

This DNA polymerase requires a protein as a primer.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.