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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)LengthDescriptionGraphical viewFeature identifierActions
Sitei12 – 121Essential for 3'-5' exonucleolysis2 Publications
Sitei14 – 141Essential for 3'-5' exonucleolysis2 Publications
Sitei15 – 151Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site1 Publication
Sitei62 – 621Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site1 Publication
Sitei65 – 651Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication
Sitei66 – 661Essential for 3'-5' exonucleolysis2 Publications
Sitei93 – 931Involved in binding template-primer structures1 Publication
Sitei122 – 1221Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication
Sitei123 – 1231Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication
Metal bindingi145 – 1451Magnesium 1Combined sources
Sitei148 – 1481Involved in the stabilization of the frayed 3' terminus at the exonuclease active site1 Publication
Metal bindingi169 – 1691Magnesium 1Combined sources
Metal bindingi249 – 2491Magnesium 2; catalyticCombined sources1 Publication
Metal bindingi250 – 2501Magnesium 2; via carbonyl oxygen; catalyticCombined sources1 Publication
Sitei252 – 2521Probably involved in binding template-primer structures1 Publication
Binding sitei254 – 2541TTP; via amide nitrogenCombined sources
Sitei254 – 2541Probably involved in nucleotide binding selection1 Publication
Sitei356 – 3561Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication
Sitei364 – 3641Involved in the binding of DNA and dNTP1 Publication
Sitei366 – 3661Stabilization of the incoming nucleotide1 Publication
Binding sitei371 – 3711TTPCombined sources
Sitei371 – 3711Interacts with the phosphate groups of the incoming nucleotide1 Publication
Sitei379 – 3791Stabilization of the incoming nucleotide1 Publication
Binding sitei383 – 3831TTPCombined sources
Sitei383 – 3831Probably involved in nucleotide binding selection1 Publication
Sitei384 – 3841Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity1 Publication
Sitei387 – 3871Probably involved in binding template-primer structures1 Publication
Sitei390 – 3901Probably involved in nucleotide binding selection1 Publication
Sitei391 – 3911Probably involved in binding template-primer structures1 Publication
Sitei420 – 4201Binds ssDNA; Essential for 3'-5' exonucleolysis1 Publication
Sitei434 – 4341Probably involved in binding template-primer structures1 Publication
Sitei438 – 4381Probably involved in binding template-primer structures1 Publication
Metal bindingi456 – 4561Magnesium 2; catalytic1 Publication
Metal bindingi458 – 4581Magnesium 2; catalyticCombined sources
Binding sitei458 – 4581TTPCombined sources
Sitei498 – 4981Probably involved in binding template-primer structures1 Publication
Sitei500 – 5001Probably involved in binding template-primer structures1 Publication
Sitei529 – 5291Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities1 Publication

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi12 – 121D → A: Strong loss of 3'-5' exonucleolysis. 2 Publications
Mutagenesisi14 – 141E → A: Strong loss of 3'-5' exonucleolysis. 2 Publications
Mutagenesisi15 – 151T → I: 95% loss of ssDNA-binding. Decreased in fidelity of DNA replication. 1 Publication
Mutagenesisi59 – 591Y → 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 Publication
Mutagenesisi59 – 591Y → 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 Publication
Mutagenesisi59 – 591Y → 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 Publication
Mutagenesisi61 – 611H → 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 Publication
Mutagenesisi61 – 611H → R: 100 fold decrease in replication activity. Complete loss of interaction with TP. 1 Publication
Mutagenesisi62 – 621N → D or H: 88% loss of ssDNA-binding. Decreased in fidelity of DNA replication. 1 Publication
Mutagenesisi65 – 651F → S: Loss of capacity to interact with a DNA primer/template structure. 1 Publication
Mutagenesisi66 – 661D → A: Strong loss of 3'-5' exonucleolysis. 2 Publications
Mutagenesisi69 – 691F → 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 Publication
Mutagenesisi69 – 691F → 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 Publication
Mutagenesisi122 – 1221S → T: Loss of capacity to interact with a DNA primer/template structure. 1 Publication
Mutagenesisi123 – 1231L → N: Loss of capacity to interact with a DNA primer/template structure. 1 Publication
Mutagenesisi128 – 1281F → A: Slight loss of interaction with TP. 1 Publication
Mutagenesisi128 – 1281F → Y: Almost complete loss of interaction with TP. 1 Publication
Mutagenesisi143 – 1431K → I or R: Strong loss of 3'-5' exonuclease, proofreading and strand-displacement activities. 1 Publication
Mutagenesisi148 – 1481Y → A: Reduced capacity to stabilize the binding of the primer terminus at the 3'-5' exonuclease active site. 1 Publication
Mutagenesisi169 – 1691D → A: Strong loss of 3'-5' exonucleolysis. 1 Publication
Mutagenesisi187 – 1871R → K: No effect on DNA-binding, TP binding and replication/amplification. 1 Publication
Mutagenesisi189 – 1891T → A: No effect on DNA-binding, TP binding and replication/amplification. 1 Publication
Mutagenesisi192 – 1921S → I: Loss of DNA-binding. Reduced TP binding. 25% loss of replication and almost complete loss of amplification. 1 Publication
Mutagenesisi192 – 1921S → N: Loss of DNA-binding. No effect on TP binding. 50% loss of replication/amplification. 1 Publication
Mutagenesisi196 – 1961K → 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 Publication
Mutagenesisi196 – 1961K → R: Slight loss of DNA-binding. No loss of replication and amplification. 1 Publication
Mutagenesisi198 – 1981F → 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 Publication
Mutagenesisi206 – 2061K → I: No effect on DNA-binding. Reduced TP binding. 70% loss of replication and 20% loss of amplification. 1 Publication
Mutagenesisi223 – 2231R → I: Favored exonucleolysis (low pol/exo ratio). 2 Publications
Mutagenesisi226 – 2261Y → 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 Publications
Mutagenesisi226 – 2261Y → S: Favored exonucleolysis. Complete loss of polymerization. 2 Publications
Mutagenesisi227 – 2271R → I: Favored exonucleolysis (low pol/exo ratio). 2 Publications
Mutagenesisi227 – 2271R → K: No effect on the pol/exo ratio. 1 Publication
Mutagenesisi228 – 2281G → A: Favored polymerization (high pol/exo ratio). 2 Publications
Mutagenesisi229 – 2291G → A: Favored exonucleolysis (low pol/exo ratio). 2 Publications
Mutagenesisi229 – 2291G → D: Favored exonucleolysis. Complete loss of polymerization. 2 Publications
Mutagenesisi230 – 2301F → A: Favored polymerization (high pol/exo ratio). 2 Publications
Mutagenesisi230 – 2301F → S: Favored exonucleolysis (low pol/exo ratio). 2 Publications
Mutagenesisi230 – 2301F → Y: No effect on the pol/exo ratio. 1 Publication
Mutagenesisi249 – 2491D → E: Complete loss of DNA polymerase activity. Slight decrease in template-primer binding. No effect on 3' to 5' exonucleolysis. 1 Publication
Mutagenesisi250 – 2501V → A: No effect on TP-DNA replication. 1 Publication
Mutagenesisi250 – 2501V → F: Complete loss of TP-DNA replication. 1 Publication
Mutagenesisi251 – 2511N → D: No effect on TP-DNA replication. 1 Publication
Mutagenesisi252 – 2521S → 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 Publication
Mutagenesisi252 – 2521S → 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 Publication
Mutagenesisi253 – 2531L → 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 Publication
Mutagenesisi254 – 2541Y → F: Decreased dNTP binding affinity. 10-fold reduced affinity for the correct nucleotide. 1 Publication
Mutagenesisi254 – 2541Y → V: Loss of discrimination for rNTPs over dNTPs. 1 Publication
Mutagenesisi255 – 2551P → 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 Publication
Mutagenesisi364 – 3641I → Q: Partial loss of hability to stably bind the DNA substrate. 1 Publication
Mutagenesisi364 – 3641I → R: Complete loss of hability to stably bind the DNA substrate. 1 Publication
Mutagenesisi366 – 3661K → 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 Publication
Mutagenesisi371 – 3711K → T: Strong decrease in the affinity for dNTPs and pyrophosphorolytic activity. No effect on exonucleolysis. 1 Publication
Mutagenesisi379 – 3791K → T: Slight increase in DNA-binding capacity. Reduced affinity for the initiating nucleotide. 1 Publication
Mutagenesisi383 – 3831K → P: Complete loss of incorporation of dNTP substrates using either DNA or TP as primer. No effect on 3' to 5' exonucleolysis. 1 Publication
Mutagenesisi383 – 3831K → 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 Publication
Mutagenesisi384 – 3841L → R: Reduced nucleotide insertion fidelity during DNA-primed polymerization and protein-primed initiation. No effect on the affinity for the different dNTPs. 1 Publication
Mutagenesisi387 – 3871N → 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 Publication
Mutagenesisi388 – 3881S → G: No effect on initiation and polymerization activities. Increased efficiency of dNTP incorporation in non-templated reactions. 1 Publication
Mutagenesisi390 – 3901Y → F: Decreased dNTP binding affinity in the post-translocation state. 4.6-fold reduced affinity for the correct nucleotide. 2 Publications
Mutagenesisi390 – 3901Y → S: Decreased dNTP binding affinity. 14-fold reduced affinity for the correct nucleotide. Loss of discrimination against dA insertion opposite 8oxodG. 2 Publications
Mutagenesisi391 – 3911G → D: Complete loss of template-primer binding. 1 Publication
Mutagenesisi392 – 3921K → Q: 50% loss of exonuclease activity. 80% loss of processivity. No effect on DNA polymerase/DNA complex formation. 1 Publication
Mutagenesisi392 – 3921K → R: 90% loss of exonuclease activity. 80% loss of processivity. No effect on DNA polymerase/DNA complex formation. 1 Publication
Mutagenesisi393 – 3931F → Y: Severe decrease in initial binding to template-primer DNA molecules. 1 Publication
Mutagenesisi434 – 4341T → N: Complete loss of TP-dAMP formation. Almost complete loss of DNA polymerization. 1 Publication
Mutagenesisi437 – 4371A → G: No effect on TP-dAMP formation. 20% loss of DNA polymerization. 1 Publication
Mutagenesisi438 – 4381R → I: Complete loss of TP-dAMP formation. Almost complete loss of DNA polymerization. 1 Publication
Mutagenesisi438 – 4381R → K: Complete loss of TP-dAMP formation. 30% loss of DNA polymerization. 1 Publication
Mutagenesisi454 – 4541Y → 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 Publication
Mutagenesisi455 – 4551C → G: 65% loss of formation of the covalent complex between the TP and 5'-dAMP. Increased 3'-5' exonucleolysis. 1 Publication
Mutagenesisi456 – 4561D → 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 Publications
Mutagenesisi457 – 4571T → P: Complete loss of initiation and polymerization activities. Severe loss of protein-priming activity. Increased 3'-5' exonucleolysis. 1 Publication
Mutagenesisi458 – 4581D → G: Complete loss of initiation and polymerization activities. Severe loss of protein-priming activity. Increased 3'-5' exonucleolysis. 1 Publication
Mutagenesisi498 – 4981K → R: Strong decrease in DNA polymerization activity. Loss of binding to a primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication
Mutagenesisi498 – 4981K → T: Strong decrease in initiation and DNA polymerization activities. Loss of binding to a primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication
Mutagenesisi500 – 5001Y → S: Strong decrease in DNA polymerization activity and interaction with primer-template DNA. Increased 3'-5' exonucleolysis. 1 Publication
Mutagenesisi529 – 5291K → A: Increased exonuclease activity and loss of primer elongation. Deficient in nucleotide incorporation. 1 Publication
Mutagenesisi529 – 5291K → E: Increased exonuclease activity and complete loss of primer elongation. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 575575DNA polymerasePRO_0000046542Add
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Sitei59 – 591Interaction with the primer terminal protein1 Publication
Sitei61 – 611Interaction with the primer terminal protein1 Publication
Sitei69 – 691Interaction with the primer terminal protein1 Publication

Structurei

Secondary structure

1
575
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 158Combined sources
Beta strandi19 – 213Combined sources
Beta strandi24 – 3310Combined sources
Beta strandi38 – 425Combined sources
Helixi44 – 5411Combined sources
Beta strandi57 – 626Combined sources
Helixi63 – 7614Combined sources
Beta strandi89 – 957Combined sources
Beta strandi100 – 11011Combined sources
Beta strandi113 – 1219Combined sources
Helixi122 – 1254Combined sources
Helixi130 – 1367Combined sources
Beta strandi148 – 1503Combined sources
Helixi160 – 18223Combined sources
Beta strandi187 – 1893Combined sources
Helixi190 – 20213Combined sources
Helixi204 – 2107Combined sources
Helixi216 – 2238Combined sources
Beta strandi231 – 2333Combined sources
Helixi235 – 2373Combined sources
Beta strandi238 – 2425Combined sources
Beta strandi244 – 2507Combined sources
Helixi253 – 2608Combined sources
Beta strandi263 – 27412Combined sources
Beta strandi283 – 29412Combined sources
Beta strandi308 – 3103Combined sources
Beta strandi324 – 3296Combined sources
Helixi330 – 33910Combined sources
Beta strandi340 – 35718Combined sources
Helixi361 – 37313Combined sources
Helixi376 – 38712Combined sources
Helixi390 – 3934Combined sources
Beta strandi401 – 4066Combined sources
Beta strandi410 – 4167Combined sources
Helixi427 – 44721Combined sources
Turni448 – 4514Combined sources
Beta strandi452 – 4565Combined sources
Beta strandi459 – 4668Combined sources
Helixi469 – 4746Combined sources
Beta strandi477 – 4793Combined sources
Beta strandi482 – 49615Combined sources
Beta strandi499 – 50911Combined sources
Beta strandi512 – 5154Combined sources
Beta strandi518 – 5203Combined sources
Beta strandi522 – 5309Combined sources
Helixi535 – 5384Combined sources
Turni543 – 5453Combined sources
Beta strandi551 – 56111Combined sources
Beta strandi564 – 57310Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 5-575.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03680.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 1911913'-5' exonuclease and strand displacement activities1 PublicationAdd
BLAST
Regioni192 – 22938Involved in DNA-binding, coordination between DNA synthesis and degradation and TP interaction3 PublicationsAdd
BLAST
Regioni230 – 562333Initiation, polymerization and pyrophosphorolytic activities1 PublicationAdd
BLAST
Regioni398 – 42023TPR21 PublicationAdd
BLAST
Regioni563 – 57513Involved in DNA-binding and TP interaction1 PublicationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi454 – 4585YCDTD1 Publication

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti492 – 4921A → V in CAA37450 (PubMed:2118623).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti176 – 1761A → R in mutant TS2(24).
Natural varianti355 – 3551A → V in mutant TS2(24).

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
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. Positions 5-575.
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: June 8, 2016
This is version 110 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.