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Protein

DNA polymerase

Gene

43

Organism
Enterobacteria phage RB69 (Bacteriophage RB69)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Replicates the viral genomic DNA. This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction for proofreading purpose.4 Publications

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).5 Publications

Cofactori

Mg2+13 Publications2 PublicationsNote: Magnesium 1 and 2 form the active site of the 3'-5' exonuclease activity (By similarity). Magnesium 3 and 4 form the active site of the polymerase activity (PubMed:23214497). Magnesium 3 is responsible for bringing the 3' hydroxyl group at the primer-terminus closer to the alpha-phosphorus atom of the incoming dNTP enabling phosphodiester bond formation (PubMed:23214497).By similarity1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi114 – 1141Magnesium 1; catalyticBy similarity
Metal bindingi116 – 1161Magnesium 1; catalyticBy similarity
Metal bindingi222 – 2221Magnesium 2; catalytic1 Publication
Metal bindingi327 – 3271Magnesium 1 and 2; catalytic1 Publication
Metal bindingi411 – 4111Magnesium 3 and 4; catalyticCombined sources9 Publications5 Publications
Metal bindingi412 – 4121Magnesium 4; via carbonyl oxygen; catalyticCombined sources3 Publications3 Publications
Binding sitei482 – 4821SubstrateCombined sources
Binding sitei560 – 5601SubstrateCombined sources
Sitei621 – 6211Optimization of metal coordination by the polymerase active site4 Publications
Metal bindingi623 – 6231Magnesium 3 and 4; catalyticCombined sources8 Publications7 Publications
Sitei706 – 7061Optimization of metal coordination by the polymerase active site, may be involved in DNA-binding2 Publications
Sitei714 – 7141Essential for viral replication1 Publication

GO - Molecular functioni

  • 3'-5' exonuclease activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: UniProtKB
  • nucleotide binding Source: InterPro

GO - Biological processi

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

Enzyme and pathway databases

SABIO-RKQ38087.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase (EC:2.7.7.75 Publications, EC:3.1.11.-3 Publications)
Alternative name(s):
Gp43
Gene namesi
Name:43
OrganismiEnterobacteria phage RB69 (Bacteriophage RB69)
Taxonomic identifieri12353 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4likevirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000000876 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi222 – 2221D → A: Complete loss of 3'-5' exonuclease activity. 1 Publication
Mutagenesisi327 – 3271D → A: Complete loss of 3'-5' exonuclease activity. 1 Publication
Mutagenesisi415 – 4151L → A or G: Decreases base selectivity by several hundred fold. 1 Publication
Mutagenesisi415 – 4151L → G or F: Increased misinsertion, increased mismatch extension and inefficient proofreading. 1 Publication
Mutagenesisi415 – 4151L → M: No effect on base selectivity. 1 Publication
Mutagenesisi561 – 5611L → A: No effect on the ability to recognize damaged DNA. Increase in probability of nucleotide incorporation. 1 Publication
Mutagenesisi565 – 5651S → G: Increased incorporation efficiency of correct dNMPs; when associated with A-567. 1 Publication
Mutagenesisi567 – 5671Y → A: Inserts both dCMP and dAMP opposite 8-oxoG rapidly and with equal efficiency. 100-fold increase of dAMP and dGMP when situated opposite guanidinohydantoin. Increased incorporation efficiency of correct dNMPs; when associated with G-565. 3 Publications
Mutagenesisi621 – 6211D → A: Drastic decrease in the efficiency of incorporation of dGMP. 1 Publication
Mutagenesisi706 – 7061K → A: Almost complete loss of polymerase activity. 1 Publication
Mutagenesisi714 – 7141D → A: Complete loss of viral replication. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 903903DNA polymerasePRO_0000046547Add
BLAST

Interactioni

Subunit structurei

Part of the replicase complex that includes the DNA polymerase, the polymerase clamp, the clamp loader complex, the single-stranded DNA binding protein, the primase, the helicase and the helicase assembly factor (By similarity). Interacts with the polymerase clamp; this interaction constitutes the polymerase holoenzyme (PubMed:10535734).By similarity1 Publication

Structurei

Secondary structure

1
903
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118Combined sources
Beta strandi14 – 207Combined sources
Beta strandi22 – 243Combined sources
Beta strandi26 – 316Combined sources
Beta strandi36 – 405Combined sources
Beta strandi43 – 453Combined sources
Beta strandi48 – 514Combined sources
Beta strandi56 – 616Combined sources
Helixi65 – 7814Combined sources
Beta strandi82 – 843Combined sources
Helixi88 – 969Combined sources
Helixi105 – 1073Combined sources
Beta strandi110 – 1167Combined sources
Beta strandi120 – 1234Combined sources
Turni126 – 1283Combined sources
Beta strandi135 – 1406Combined sources
Turni141 – 1444Combined sources
Beta strandi145 – 1517Combined sources
Beta strandi152 – 1565Combined sources
Helixi164 – 1685Combined sources
Helixi171 – 1733Combined sources
Turni176 – 1794Combined sources
Helixi180 – 1834Combined sources
Beta strandi186 – 1938Combined sources
Helixi194 – 20714Combined sources
Beta strandi211 – 2144Combined sources
Turni218 – 2214Combined sources
Helixi222 – 23413Combined sources
Helixi236 – 2394Combined sources
Helixi240 – 2423Combined sources
Beta strandi248 – 2558Combined sources
Beta strandi258 – 2658Combined sources
Beta strandi269 – 2724Combined sources
Helixi273 – 2808Combined sources
Helixi290 – 2989Combined sources
Helixi309 – 3113Combined sources
Helixi312 – 33827Combined sources
Helixi340 – 35112Combined sources
Helixi355 – 3595Combined sources
Helixi361 – 37414Combined sources
Turni375 – 3773Combined sources
Beta strandi402 – 4043Combined sources
Beta strandi405 – 4128Combined sources
Helixi415 – 4239Combined sources
Helixi427 – 4293Combined sources
Beta strandi430 – 4334Combined sources
Helixi439 – 4435Combined sources
Beta strandi452 – 4565Combined sources
Beta strandi460 – 4634Combined sources
Beta strandi465 – 4673Combined sources
Helixi470 – 50233Combined sources
Beta strandi503 – 5053Combined sources
Beta strandi507 – 5093Combined sources
Beta strandi518 – 5203Combined sources
Helixi524 – 5307Combined sources
Beta strandi531 – 5333Combined sources
Helixi535 – 56935Combined sources
Helixi580 – 60930Combined sources
Beta strandi617 – 6215Combined sources
Beta strandi624 – 6285Combined sources
Helixi630 – 6367Combined sources
Helixi638 – 6403Combined sources
Helixi644 – 65714Combined sources
Helixi659 – 67315Combined sources
Beta strandi683 – 6897Combined sources
Beta strandi693 – 6953Combined sources
Beta strandi700 – 7045Combined sources
Beta strandi707 – 7159Combined sources
Beta strandi718 – 73013Combined sources
Helixi731 – 7333Combined sources
Helixi739 – 75416Combined sources
Helixi757 – 77014Combined sources
Helixi771 – 7733Combined sources
Helixi776 – 7794Combined sources
Beta strandi781 – 7844Combined sources
Helixi789 – 7913Combined sources
Beta strandi792 – 7976Combined sources
Helixi803 – 81412Combined sources
Turni815 – 8173Combined sources
Beta strandi819 – 8213Combined sources
Beta strandi828 – 8358Combined sources
Beta strandi837 – 8393Combined sources
Beta strandi842 – 8498Combined sources
Helixi856 – 86510Combined sources
Helixi868 – 8758Combined sources
Helixi877 – 88711Combined sources
Beta strandi891 – 8944Combined sources
Helixi897 – 9004Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B1Fmodel-R387-892[»]
1B8HX-ray3.00D893-903[»]
1CLQX-ray2.70A1-903[»]
1IG9X-ray2.60A1-903[»]
1IH7X-ray2.21A1-903[»]
1Q9XX-ray2.69A/B/C/D1-903[»]
1Q9YX-ray2.80A1-903[»]
1QE4model-F1-903[»]
1WAFX-ray3.20A/B1-903[»]
1WAGmodel-R1-903[»]
1WAHmodel-R1-903[»]
1WAImodel-R1-903[»]
1WAJX-ray2.80A1-903[»]
2ATQX-ray3.20A1-903[»]
2DTUX-ray2.37A/B/C/D1-902[»]
2DY4X-ray2.65A/B/C/D1-903[»]
2OYQX-ray2.86A/B/C/D1-903[»]
2OZMX-ray2.86A1-903[»]
2OZSX-ray2.75A1-903[»]
2P5GX-ray2.80A/B/C/D1-903[»]
2P5OX-ray2.80A/B/C/D1-903[»]
3CFOX-ray2.60A1-903[»]
3CFPX-ray2.50A1-903[»]
3CFRX-ray2.40A1-903[»]
3CQ8X-ray2.50A1-903[»]
3KD1X-ray2.66E1-903[»]
3KD5X-ray2.69E1-903[»]
3L8BX-ray2.15A/B1-903[»]
3LDSX-ray3.00A1-903[»]
3LZIX-ray2.30A1-903[»]
3LZJX-ray2.05A1-903[»]
3NAEX-ray2.00A1-903[»]
3NCIX-ray1.79A1-903[»]
3NDKX-ray2.00A1-903[»]
3NE6X-ray2.00A1-903[»]
3NGIX-ray1.89A1-903[»]
3NHGX-ray2.50A1-903[»]
3QEIX-ray2.18A1-903[»]
3QEPX-ray1.80A1-903[»]
3QERX-ray1.96A1-903[»]
3QESX-ray1.98A1-903[»]
3QETX-ray2.08A1-903[»]
3QEVX-ray1.77A1-903[»]
3QEWX-ray1.84A1-903[»]
3QEXX-ray1.73A1-903[»]
3QNNX-ray1.92A1-901[»]
3QNOX-ray1.88A1-901[»]
3RMAX-ray2.84A/B/C/D1-903[»]
3RMBX-ray2.65A/B/C/D1-903[»]
3RMCX-ray3.00A/B/C/D1-903[»]
3RMDX-ray2.98A/B/C/D1-903[»]
3RWUX-ray2.33A1-901[»]
3S9HX-ray1.95A1-903[»]
3SCXX-ray2.35A1-901[»]
3SI6X-ray1.85A1-901[»]
3SJJX-ray2.38A1-901[»]
3SNNX-ray2.00A1-901[»]
3SPYX-ray2.14A1-901[»]
3SPZX-ray2.43A1-903[»]
3SQ0X-ray2.00A1-903[»]
3SQ1X-ray1.82A1-901[»]
3SQ2X-ray2.10A1-902[»]
3SQ4X-ray2.23A1-902[»]
3SUNX-ray2.42A1-895[»]
3SUOX-ray2.23A1-900[»]
3SUPX-ray2.32A1-903[»]
3SUQX-ray3.15A1-897[»]
3TABX-ray2.80A/B/C/D1-903[»]
3TAEX-ray2.71A/B/C/D1-903[»]
3TAFX-ray3.00A/B/C/D1-903[»]
3TAGX-ray2.95A/B/C/D1-903[»]
3UIQX-ray1.88A1-903[»]
4DTJX-ray1.90A1-901[»]
4DTMX-ray1.95A1-901[»]
4DTNX-ray1.96A1-903[»]
4DTOX-ray2.05A1-903[»]
4DTPX-ray2.05A1-903[»]
4DTRX-ray2.04A1-903[»]
4DTSX-ray1.96A1-903[»]
4DTUX-ray1.86A1-903[»]
4DTXX-ray1.84A1-903[»]
4DU1X-ray2.15A1-903[»]
4DU3X-ray2.02A1-903[»]
4DU4X-ray2.28A1-903[»]
4E3SX-ray2.04A1-903[»]
4FJ5X-ray2.05A1-903[»]
4FJ7X-ray1.90A1-903[»]
4FJ8X-ray2.19A1-903[»]
4FJ9X-ray1.97A1-903[»]
4FJGX-ray2.02A1-903[»]
4FJHX-ray2.11A1-903[»]
4FJIX-ray2.20A1-903[»]
4FJJX-ray1.99A1-903[»]
4FJKX-ray2.00A1-903[»]
4FJLX-ray1.87A1-903[»]
4FJMX-ray2.02A1-903[»]
4FJNX-ray1.98A1-903[»]
4FJXX-ray2.11A1-903[»]
4FK0X-ray2.18A1-903[»]
4FK2X-ray1.98A1-903[»]
4FK4X-ray1.90A1-903[»]
4I9LX-ray2.60A1-903[»]
4I9QX-ray2.30A/B1-903[»]
4J2AX-ray1.80A1-901[»]
4J2BX-ray2.04A1-901[»]
4J2DX-ray1.76A1-901[»]
4J2EX-ray2.02A1-901[»]
4KHNX-ray2.55A/B1-903[»]
4KHQX-ray2.19A1-903[»]
4KHSX-ray2.12A1-903[»]
4KHUX-ray2.05A1-903[»]
4KHWX-ray2.37A1-903[»]
4KHYX-ray2.25A1-903[»]
4KI4X-ray2.45A1-903[»]
4KI6X-ray2.55A1-903[»]
4M3RX-ray2.07A1-903[»]
4M3TX-ray1.90A1-903[»]
4M3UX-ray2.07A1-903[»]
4M3WX-ray2.10A1-903[»]
4M3XX-ray2.20A1-903[»]
4M3YX-ray1.86A1-903[»]
4M3ZX-ray1.84A1-903[»]
4M41X-ray2.15A1-903[»]
4M42X-ray2.04A1-903[»]
4M45X-ray1.89A1-903[»]
ProteinModelPortaliQ38087.
SMRiQ38087. Positions 1-903.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ38087.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni103 – 3402383'-5'exonuclease1 PublicationAdd
BLAST
Regioni248 – 26417Beta hairpin1 PublicationAdd
BLAST
Regioni380 – 903524Polymerase1 PublicationAdd
BLAST
Regioni414 – 4163Substrate bindingCombined sources
Regioni705 – 7084Binding of DNA in B-conformation2 Publications
Regioni897 – 9026Interaction with the polymerase clampBy similarity

Domaini

The N-terminus contains the 3'-5' exonuclease activity (PubMed:9215631). The C-terminus contains the polymerase activity and is involved in binding to the polymerase clamp protein (PubMed:9215631). A beta hairpin structure is necessary for the proofreading function of the polymerase (By similarity).By similarity1 Publication

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

Phylogenomic databases

KOiK18942.

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.
IPR006133. DNA-dir_DNA_pol_B_exonuc.
IPR006134. DNA-dir_DNA_pol_B_multi_dom.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q38087-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKEFYLTVEQ IGDSIFERYI DSNGRERTRE VEYKPSLFAH CPESQATKYF
60 70 80 90 100
DIYGKPCTRK LFANMRDASQ WIKRMEDIGL EALGMDDFKL AYLSDTYNYE
110 120 130 140 150
IKYDHTKIRV ANFDIEVTSP DGFPEPSQAK HPIDAITHYD SIDDRFYVFD
160 170 180 190 200
LLNSPYGNVE EWSIEIAAKL QEQGGDEVPS EIIDKIIYMP FDNEKELLME
210 220 230 240 250
YLNFWQQKTP VILTGWNVES FDIPYVYNRI KNIFGESTAK RLSPHRKTRV
260 270 280 290 300
KVIENMYGSR EIITLFGISV LDYIDLYKKF SFTNQPSYSL DYISEFELNV
310 320 330 340 350
GKLKYDGPIS KLRESNHQRY ISYNIIDVYR VLQIDAKRQF INLSLDMGYY
360 370 380 390 400
AKIQIQSVFS PIKTWDAIIF NSLKEQNKVI PQGRSHPVQP YPGAFVKEPI
410 420 430 440 450
PNRYKYVMSF DLTSLYPSII RQVNISPETI AGTFKVAPLH DYINAVAERP
460 470 480 490 500
SDVYSCSPNG MMYYKDRDGV VPTEITKVFN QRKEHKGYML AAQRNGEIIK
510 520 530 540 550
EALHNPNLSV DEPLDVDYRF DFSDEIKEKI KKLSAKSLNE MLFRAQRTEV
560 570 580 590 600
AGMTAQINRK LLINSLYGAL GNVWFRYYDL RNATAITTFG QMALQWIERK
610 620 630 640 650
VNEYLNEVCG TEGEAFVLYG DTDSIYVSAD KIIDKVGESK FRDTNHWVDF
660 670 680 690 700
LDKFARERME PAIDRGFREM CEYMNNKQHL MFMDREAIAG PPLGSKGIGG
710 720 730 740 750
FWTGKKRYAL NVWDMEGTRY AEPKLKIMGL ETQKSSTPKA VQKALKECIR
760 770 780 790 800
RMLQEGEESL QEYFKEFEKE FRQLNYISIA SVSSANNIAK YDVGGFPGPK
810 820 830 840 850
CPFHIRGILT YNRAIKGNID APQVVEGEKV YVLPLREGNP FGDKCIAWPS
860 870 880 890 900
GTEITDLIKD DVLHWMDYTV LLEKTFIKPL EGFTSAAKLD YEKKASLFDM

FDF
Length:903
Mass (Da):104,613
Last modified:November 1, 1996 - v1
Checksum:iA3983FC16D4C0509
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U34036 Genomic DNA. Translation: AAA93077.1.
AY303349 Genomic DNA. Translation: AAP75958.1.
RefSeqiNP_861746.1. NC_004928.1.

Genome annotation databases

GeneIDi1494172.
KEGGivg:1494172.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U34036 Genomic DNA. Translation: AAA93077.1.
AY303349 Genomic DNA. Translation: AAP75958.1.
RefSeqiNP_861746.1. NC_004928.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B1Fmodel-R387-892[»]
1B8HX-ray3.00D893-903[»]
1CLQX-ray2.70A1-903[»]
1IG9X-ray2.60A1-903[»]
1IH7X-ray2.21A1-903[»]
1Q9XX-ray2.69A/B/C/D1-903[»]
1Q9YX-ray2.80A1-903[»]
1QE4model-F1-903[»]
1WAFX-ray3.20A/B1-903[»]
1WAGmodel-R1-903[»]
1WAHmodel-R1-903[»]
1WAImodel-R1-903[»]
1WAJX-ray2.80A1-903[»]
2ATQX-ray3.20A1-903[»]
2DTUX-ray2.37A/B/C/D1-902[»]
2DY4X-ray2.65A/B/C/D1-903[»]
2OYQX-ray2.86A/B/C/D1-903[»]
2OZMX-ray2.86A1-903[»]
2OZSX-ray2.75A1-903[»]
2P5GX-ray2.80A/B/C/D1-903[»]
2P5OX-ray2.80A/B/C/D1-903[»]
3CFOX-ray2.60A1-903[»]
3CFPX-ray2.50A1-903[»]
3CFRX-ray2.40A1-903[»]
3CQ8X-ray2.50A1-903[»]
3KD1X-ray2.66E1-903[»]
3KD5X-ray2.69E1-903[»]
3L8BX-ray2.15A/B1-903[»]
3LDSX-ray3.00A1-903[»]
3LZIX-ray2.30A1-903[»]
3LZJX-ray2.05A1-903[»]
3NAEX-ray2.00A1-903[»]
3NCIX-ray1.79A1-903[»]
3NDKX-ray2.00A1-903[»]
3NE6X-ray2.00A1-903[»]
3NGIX-ray1.89A1-903[»]
3NHGX-ray2.50A1-903[»]
3QEIX-ray2.18A1-903[»]
3QEPX-ray1.80A1-903[»]
3QERX-ray1.96A1-903[»]
3QESX-ray1.98A1-903[»]
3QETX-ray2.08A1-903[»]
3QEVX-ray1.77A1-903[»]
3QEWX-ray1.84A1-903[»]
3QEXX-ray1.73A1-903[»]
3QNNX-ray1.92A1-901[»]
3QNOX-ray1.88A1-901[»]
3RMAX-ray2.84A/B/C/D1-903[»]
3RMBX-ray2.65A/B/C/D1-903[»]
3RMCX-ray3.00A/B/C/D1-903[»]
3RMDX-ray2.98A/B/C/D1-903[»]
3RWUX-ray2.33A1-901[»]
3S9HX-ray1.95A1-903[»]
3SCXX-ray2.35A1-901[»]
3SI6X-ray1.85A1-901[»]
3SJJX-ray2.38A1-901[»]
3SNNX-ray2.00A1-901[»]
3SPYX-ray2.14A1-901[»]
3SPZX-ray2.43A1-903[»]
3SQ0X-ray2.00A1-903[»]
3SQ1X-ray1.82A1-901[»]
3SQ2X-ray2.10A1-902[»]
3SQ4X-ray2.23A1-902[»]
3SUNX-ray2.42A1-895[»]
3SUOX-ray2.23A1-900[»]
3SUPX-ray2.32A1-903[»]
3SUQX-ray3.15A1-897[»]
3TABX-ray2.80A/B/C/D1-903[»]
3TAEX-ray2.71A/B/C/D1-903[»]
3TAFX-ray3.00A/B/C/D1-903[»]
3TAGX-ray2.95A/B/C/D1-903[»]
3UIQX-ray1.88A1-903[»]
4DTJX-ray1.90A1-901[»]
4DTMX-ray1.95A1-901[»]
4DTNX-ray1.96A1-903[»]
4DTOX-ray2.05A1-903[»]
4DTPX-ray2.05A1-903[»]
4DTRX-ray2.04A1-903[»]
4DTSX-ray1.96A1-903[»]
4DTUX-ray1.86A1-903[»]
4DTXX-ray1.84A1-903[»]
4DU1X-ray2.15A1-903[»]
4DU3X-ray2.02A1-903[»]
4DU4X-ray2.28A1-903[»]
4E3SX-ray2.04A1-903[»]
4FJ5X-ray2.05A1-903[»]
4FJ7X-ray1.90A1-903[»]
4FJ8X-ray2.19A1-903[»]
4FJ9X-ray1.97A1-903[»]
4FJGX-ray2.02A1-903[»]
4FJHX-ray2.11A1-903[»]
4FJIX-ray2.20A1-903[»]
4FJJX-ray1.99A1-903[»]
4FJKX-ray2.00A1-903[»]
4FJLX-ray1.87A1-903[»]
4FJMX-ray2.02A1-903[»]
4FJNX-ray1.98A1-903[»]
4FJXX-ray2.11A1-903[»]
4FK0X-ray2.18A1-903[»]
4FK2X-ray1.98A1-903[»]
4FK4X-ray1.90A1-903[»]
4I9LX-ray2.60A1-903[»]
4I9QX-ray2.30A/B1-903[»]
4J2AX-ray1.80A1-901[»]
4J2BX-ray2.04A1-901[»]
4J2DX-ray1.76A1-901[»]
4J2EX-ray2.02A1-901[»]
4KHNX-ray2.55A/B1-903[»]
4KHQX-ray2.19A1-903[»]
4KHSX-ray2.12A1-903[»]
4KHUX-ray2.05A1-903[»]
4KHWX-ray2.37A1-903[»]
4KHYX-ray2.25A1-903[»]
4KI4X-ray2.45A1-903[»]
4KI6X-ray2.55A1-903[»]
4M3RX-ray2.07A1-903[»]
4M3TX-ray1.90A1-903[»]
4M3UX-ray2.07A1-903[»]
4M3WX-ray2.10A1-903[»]
4M3XX-ray2.20A1-903[»]
4M3YX-ray1.86A1-903[»]
4M3ZX-ray1.84A1-903[»]
4M41X-ray2.15A1-903[»]
4M42X-ray2.04A1-903[»]
4M45X-ray1.89A1-903[»]
ProteinModelPortaliQ38087.
SMRiQ38087. Positions 1-903.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1494172.
KEGGivg:1494172.

Phylogenomic databases

KOiK18942.

Enzyme and pathway databases

SABIO-RKQ38087.

Miscellaneous databases

EvolutionaryTraceiQ38087.

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.
IPR006133. DNA-dir_DNA_pol_B_exonuc.
IPR006134. DNA-dir_DNA_pol_B_multi_dom.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Modular organization of T4 DNA polymerase. Evidence from phylogenetics."
    Wang C.C., Yeh L.-S., Karam J.D.
    J. Biol. Chem. 270:26558-26564(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Enterobacteria phage RB69 complete genome."
    Petrov V., Nolan J., Chin D., Letarov A., Krisch H.M., Karam J.D.
    Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives."
    Mueser T.C., Hinerman J.M., Devos J.M., Boyer R.A., Williams K.J.
    Virol. J. 7:359-359(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  4. "Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69."
    Wang J., Sattar A.K., Wang C.C., Karam J.D., Konigsberg W.H., Steitz T.A.
    Cell 89:1087-1099(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), DOMAIN.
  5. "Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex."
    Shamoo Y., Steitz T.A.
    Cell 99:155-166(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH THE POLYMERASE CLAMP, INTERACTION WITH THE POLYMERASE CLAMP.
  6. "Structure of the replicating complex of a pol alpha family DNA polymerase."
    Franklin M.C., Wang J., Steitz T.A.
    Cell 105:657-667(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP, COFACTOR.
  7. "Lesion (in)tolerance reveals insights into DNA replication fidelity."
    Freisinger E., Grollman A.P., Miller H., Kisker C.
    EMBO J. 23:1494-1505(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.69 ANGSTROMS) IN COMPLEX WITH CALCIUM, COFACTOR.
  8. "Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site."
    Hogg M., Wallace S.S., Doublie S.
    EMBO J. 23:1483-1493(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS), COFACTOR.
  9. "Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide."
    Zahn K.E., Belrhali H., Wallace S.S., Doublie S.
    Biochemistry 46:10551-10561(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, COFACTOR.
  10. "Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family."
    Hogg M., Aller P., Konigsberg W., Wallace S.S., Doublie S.
    J. Biol. Chem. 282:1432-1444(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) OF 1-902, CATALYTIC ACTIVITY, FUNCTION.
  11. "A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol."
    Aller P., Rould M.A., Hogg M., Wallace S.S., Doublie S.
    Proc. Natl. Acad. Sci. U.S.A. 104:814-818(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS).
  12. "Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity."
    Zhong X., Pedersen L.C., Kunkel T.A.
    Nucleic Acids Res. 36:3892-3904(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH CALCIUM; DNA AND TTP, FUNCTION, COFACTOR, CATALYTIC ACTIVITY, MUTAGENESIS OF LEU-415.
  13. "Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69."
    Hogg M., Rudnicki J., Midkiff J., Reha-Krantz L., Doublie S., Wallace S.S.
    Biochemistry 49:2317-2325(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEX WITH MANGANESE, MUTAGENESIS OF LEU-561, COFACTOR.
  14. "Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin."
    Aller P., Ye Y., Wallace S.S., Burrows C.J., Doublie S.
    Biochemistry 49:2502-2509(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS), COFACTOR.
  15. "Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine."
    Beckman J., Wang M., Blaha G., Wang J., Konigsberg W.H.
    Biochemistry 49:4116-4125(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH CTP AND CALCIUM, MUTAGENESIS OF TYR-567.
  16. "Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP and dGMP to be inserted opposite Guanidinohydantoin."
    Beckman J., Wang M., Blaha G., Wang J., Konigsberg W.H.
    Biochemistry 49:8554-8563(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH CALCIUM, MUTAGENESIS OF TYR-567, CATALYTIC ACTIVITY.
  17. "Structure of the 2-aminopurine-cytosine base pair formed in the polymerase active site of the RB69 Y567A-DNA polymerase."
    Reha-Krantz L.J., Hariharan C., Subuddhi U., Xia S., Zhao C., Beckman J., Christian T., Konigsberg W.
    Biochemistry 50:10136-10149(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 1-902 IN COMPLEX WITH DNA AND TTP, MUTAGENESIS OF TYR-567.
  18. "The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site."
    Zahn K.E., Averill A., Wallace S.S., Doublie S.
    Biochemistry 50:10350-10358(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.71 ANGSTROMS), COFACTOR.
  19. "Insights into base selectivity from the 1.8 A resolution structure of an RB69 DNA polymerase ternary complex."
    Wang M., Xia S., Blaha G., Steitz T.A., Konigsberg W.H., Wang J.
    Biochemistry 50:581-590(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) IN COMPLEX WITH CALCIUM, COFACTOR.
  20. "Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase."
    Xia S., Wang M., Blaha G., Konigsberg W.H., Wang J.
    Biochemistry 50:9114-9124(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.82 ANGSTROMS) OF 1-901 IN COMPLEXES WITH MAGNESIUM AND MANGANESE, COFACTOR.
  21. "Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex."
    Xia S., Konigsberg W.H., Wang J.
    J. Am. Chem. Soc. 133:10003-10005(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH ATP; CALCIUM AND TTP.
  22. "Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase."
    Zahn K.E., Tchesnokov E.P., Gotte M., Doublie S.
    J. Biol. Chem. 286:25246-25255(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.66 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, COFACTOR.
  23. "Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures."
    Xia S., Wang M., Lee H.R., Sinha A., Blaha G., Christian T., Wang J., Konigsberg W.
    J. Mol. Biol. 406:558-570(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP, MUTAGENESIS OF SER-565 AND TYR-567.
  24. "A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex."
    Aller P., Duclos S., Wallace S.S., Doublie S.
    J. Mol. Biol. 412:22-34(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS).
  25. "Structural basis for differential insertion kinetics of dNMPs opposite a difluorotoluene nucleotide residue."
    Xia S., Eom S.H., Konigsberg W.H., Wang J.
    Biochemistry 51:1476-1485(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) IN COMPLEX WITH CALCIUM.
  26. "Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA."
    Xia S., Christian T.D., Wang J., Konigsberg W.H.
    Biochemistry 51:4343-4353(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.02 ANGSTROMS) IN COMPLEX WITH CALCIUM, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-621 AND LYS-706, COFACTOR.
  27. "Using a fluorescent cytosine analogue tC(o) to probe the effect of the Y567 to Ala substitution on the preinsertion steps of dNMP incorporation by RB69 DNA polymerase."
    Xia S., Beckman J., Wang J., Konigsberg W.H.
    Biochemistry 51:4609-4617(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) OF 1-901 IN COMPLEX WITH ATP AND CALCIUM, MUTAGENESIS OF TYR-567.
  28. "Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA."
    Xia S., Vashishtha A., Bulkley D., Eom S.H., Wang J., Konigsberg W.H.
    Biochemistry 51:4922-4931(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) IN COMPLEXES WITH CALCIUM; DNA; ATP; CTP; GTP AND TTP, CATALYTIC ACTIVITY, FUNCTION.
  29. "Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase."
    Xia S., Eom S.H., Konigsberg W.H., Wang J.
    Protein Sci. 21:447-451(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) IN COMPLEX WITH CALCIUM, COFACTOR.
  30. "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase."
    Xia S., Wang J., Konigsberg W.H.
    J. Am. Chem. Soc. 135:193-202(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP, COFACTOR, MUTAGENESIS OF ASP-222 AND ASP-327, CATALYTIC ACTIVITY.
  31. "Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics."
    Xia S., Wood M., Bradley M.J., De La Cruz E.M., Konigsberg W.H.
    Nucleic Acids Res. 41:9077-9089(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 1-901 IN COMPLEX WITH ATP; CALCIUM AND TTP, MUTAGENESIS OF LEU-415, COFACTOR.
  32. "A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site."
    Jacewicz A., Trzemecka A., Guja K.E., Plochocka D., Yakubovskaya E., Bebenek A., Garcia-Diaz M.
    PLoS ONE 8:76700-76700(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), MUTAGENESIS OF ASP-714, CATALYTIC ACTIVITY, COFACTOR.
  33. "Structure-function analysis of ribonucleotide bypass by B family DNA replicases."
    Clausen A.R., Murray M.S., Passer A.R., Pedersen L.C., Kunkel T.A.
    Proc. Natl. Acad. Sci. U.S.A. 110:16802-16807(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP.
  34. "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant."
    Xia S., Konigsberg W.H.
    Protein Sci. 23:508-513(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) IN COMPLEX WITH ATP AND CALCIUM.

Entry informationi

Entry nameiDPOL_BPR69
AccessioniPrimary (citable) accession number: Q38087
Secondary accession number(s): Q76XX8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme

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.