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Protein

DNA polymerase

Gene

polA

Organism
Geobacillus kaustophilus (strain HTA426)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei617 – 6171CTPCombined sources
Binding sitei631 – 6311CTPCombined sources
Metal bindingi655 – 6551MagnesiumCombined sources
Metal bindingi655 – 6551ManganeseCombined sources
Metal bindingi656 – 6561Magnesium; via carbonyl oxygenCombined sources
Metal bindingi656 – 6561Manganese; via carbonyl oxygenCombined sources
Binding sitei658 – 6581CTPCombined sources
Binding sitei684 – 6841CTPCombined sources
Binding sitei704 – 7041CTPCombined sources
Binding sitei708 – 7081CTPCombined sources
Binding sitei712 – 7121CTPCombined sources
Binding sitei716 – 7161CTPCombined sources
Metal bindingi832 – 8321MagnesiumCombined sources
Metal bindingi832 – 8321ManganeseCombined sources
Binding sitei832 – 8321CTPCombined sources

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi471 – 4755CTPCombined sources
Nucleotide bindingi769 – 7702CTPCombined sources

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymeraseImported, Hydrolase, NucleaseSAAS annotation, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replicationUniRule annotation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotation, MagnesiumCombined sources, ManganeseCombined sources, Metal-bindingCombined sources, Nucleotide-bindingCombined sources

Enzyme and pathway databases

BioCyciGKAU235909:GJO7-2825-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymeraseUniRule annotation (EC:2.7.7.7UniRule annotation)
Gene namesi
Name:polAImported
Ordered Locus Names:GK2730Imported
OrganismiGeobacillus kaustophilus (strain HTA426)Imported
Taxonomic identifieri235909 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus
ProteomesiUP000001172 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi235909.GK2730.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NJWX-ray1.90A299-878[»]
1UA0X-ray2.10A299-878[»]
2HHUX-ray1.80A300-878[»]
2HHVX-ray1.55A300-878[»]
2HHWX-ray1.88A/D299-878[»]
2HHXX-ray2.26A300-878[»]
2HVIX-ray1.98A/D300-878[»]
3HP6X-ray1.81A/D299-878[»]
3PV8X-ray1.52A/D287-878[»]
3PX0X-ray1.73A/D287-878[»]
3PX4X-ray1.58A/D287-878[»]
3PX6X-ray1.59A/D287-878[»]
4DQIX-ray1.69A/D287-878[»]
4DQPX-ray1.74A/D287-878[»]
4DQQX-ray1.59A/D287-878[»]
4DQRX-ray1.95A/D287-878[»]
4DQSX-ray1.66A287-878[»]
4DS4X-ray1.68A/D287-878[»]
4DS5X-ray1.68A/D287-878[»]
4DSEX-ray1.67A/D287-878[»]
4DSFX-ray1.66A/D287-878[»]
4E0DX-ray1.58A287-878[»]
4EZ6X-ray1.64A/D287-878[»]
4EZ9X-ray1.64A/D287-878[»]
4F2RX-ray1.63A/D287-878[»]
4F2SX-ray1.65A/D287-878[»]
4F3OX-ray1.57A/D287-878[»]
4F4KX-ray1.60A/D287-878[»]
4F8RX-ray1.64A/D287-878[»]
ProteinModelPortaliQ5KWC1.
SMRiQ5KWC1. Positions 299-878.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5KWC1.

Family & Domainsi

Sequence similaritiesi

Belongs to the DNA polymerase type-A family.UniRule annotation
Contains 5'-3' exonuclease domain.SAAS annotation

Phylogenomic databases

HOGENOMiHOG000020998.
KOiK02335.
OMAiKANRPPM.
OrthoDBiEOG6SJJH7.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.40.50.1010. 1 hit.
InterProiIPR002562. 3'-5'_exonuclease_dom.
IPR020046. 5-3_exonucl_a-hlix_arch_N.
IPR020045. 5-3_exonuclease_C.
IPR002421. 5-3_exonuclease_N.
IPR019760. DNA-dir_DNA_pol_A_CS.
IPR001098. DNA-dir_DNA_pol_A_palm_dom.
IPR018320. DNA_polymerase_1.
IPR002298. DNA_polymerase_A.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF01367. 5_3_exonuc. 1 hit.
PF02739. 5_3_exonuc_N. 1 hit.
PF00476. DNA_pol_A. 1 hit.
[Graphical view]
PRINTSiPR00868. DNAPOLI.
SMARTiSM00474. 35EXOc. 1 hit.
SM00475. 53EXOc. 1 hit.
SM00279. HhH2. 1 hit.
SM00482. POLAc. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 1 hit.
SSF53098. SSF53098. 1 hit.
SSF88723. SSF88723. 1 hit.
TIGRFAMsiTIGR00593. pola. 1 hit.
PROSITEiPS00447. DNA_POLYMERASE_A. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5KWC1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLKKKLVLI DGSSVAYRAF FALPLLHNDK GIHTNAVYGF TMMLNKILAE
60 70 80 90 100
EEPTHMLVAF DAGKTTFRHE AFQEYKGGRQ QTPPELSEQF PLLRELLRAY
110 120 130 140 150
RIPAYELENY EADDIIGTLA ARAEQEGFEV KVISGDRDLT QLASPHVTVD
160 170 180 190 200
ITKKGITDIE PYTPETVREK YGLTPEQIVD LKGLMGDKSD NIPGVPGIGE
210 220 230 240 250
KTAVKLLRQF GTVENVLASI DEIKGEKLKE TLRQHREMAL LSKKLAAIRR
260 270 280 290 300
DAPVELSLDD IVYQGEDREK VVALFKELGF QSFLEKMESP SSEEEKPLAK
310 320 330 340 350
MAFTLADRVT EEMLADKAAL VVEVVEENYH DAPIVGIAVV NEHGRFFLRP
360 370 380 390 400
ETALADPQFV AWLGDETKKK SMFDSKRAAV ALKWKGIELC GVSFDLLLAA
410 420 430 440 450
YLLDPAQGVD DVAAAAKMKQ YEAVRPDEAV YGKGAKRAVP DEPVLAEHLV
460 470 480 490 500
RKAAAIWELE RPFLDELRRN EQDRLLVELE QPLSSILAEM EFAGVKVDTK
510 520 530 540 550
RLEQMGKELA EQLGTVEQRI YELAGQEFNI NSPKQLGVIL FEKLQLPVLK
560 570 580 590 600
KTKTGYSTSA DVLEKLAPYH EIVENILHYR QLGKLQSTYI EGLLKVVRPD
610 620 630 640 650
TKKVHTIFNQ ALTQTGRLSS TEPNLQNIPI RLEEGRKIRQ AFVPSESDWL
660 670 680 690 700
IFAADYSQIE LRVLAHIAED DNLMEAFRRD LDIHTKTAMD IFQVSEDEVT
710 720 730 740 750
PNMRRQAKAV NFGIVYGISD YGLAQNLNIS RKEAAEFIER YFESFPGVKR
760 770 780 790 800
YMENIVQEAK QKGYVTTLLH RRRYLPDITS RNFNVRSFAE RMAMNTPIQG
810 820 830 840 850
SAADIIKKAM IDLNARLKEE RLQARLLLQV HDELILEAPK EEMERLCRLV
860 870
PEVMEQAVTL RVPLKVDYHY GSTWYDAK
Length:878
Mass (Da):99,646
Last modified:February 1, 2005 - v1
Checksum:iD50E58940CE21B01
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD77015.1.
RefSeqiWP_011232204.1. NC_006510.1.
YP_148583.1. NC_006510.1.

Genome annotation databases

EnsemblBacteriaiBAD77015; BAD77015; GK2730.
GeneIDi3184068.
KEGGigka:GK2730.
PATRICi21966931. VBIGeoKau81518_2914.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD77015.1.
RefSeqiWP_011232204.1. NC_006510.1.
YP_148583.1. NC_006510.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NJWX-ray1.90A299-878[»]
1UA0X-ray2.10A299-878[»]
2HHUX-ray1.80A300-878[»]
2HHVX-ray1.55A300-878[»]
2HHWX-ray1.88A/D299-878[»]
2HHXX-ray2.26A300-878[»]
2HVIX-ray1.98A/D300-878[»]
3HP6X-ray1.81A/D299-878[»]
3PV8X-ray1.52A/D287-878[»]
3PX0X-ray1.73A/D287-878[»]
3PX4X-ray1.58A/D287-878[»]
3PX6X-ray1.59A/D287-878[»]
4DQIX-ray1.69A/D287-878[»]
4DQPX-ray1.74A/D287-878[»]
4DQQX-ray1.59A/D287-878[»]
4DQRX-ray1.95A/D287-878[»]
4DQSX-ray1.66A287-878[»]
4DS4X-ray1.68A/D287-878[»]
4DS5X-ray1.68A/D287-878[»]
4DSEX-ray1.67A/D287-878[»]
4DSFX-ray1.66A/D287-878[»]
4E0DX-ray1.58A287-878[»]
4EZ6X-ray1.64A/D287-878[»]
4EZ9X-ray1.64A/D287-878[»]
4F2RX-ray1.63A/D287-878[»]
4F2SX-ray1.65A/D287-878[»]
4F3OX-ray1.57A/D287-878[»]
4F4KX-ray1.60A/D287-878[»]
4F8RX-ray1.64A/D287-878[»]
ProteinModelPortaliQ5KWC1.
SMRiQ5KWC1. Positions 299-878.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi235909.GK2730.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD77015; BAD77015; GK2730.
GeneIDi3184068.
KEGGigka:GK2730.
PATRICi21966931. VBIGeoKau81518_2914.

Phylogenomic databases

HOGENOMiHOG000020998.
KOiK02335.
OMAiKANRPPM.
OrthoDBiEOG6SJJH7.

Enzyme and pathway databases

BioCyciGKAU235909:GJO7-2825-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ5KWC1.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.40.50.1010. 1 hit.
InterProiIPR002562. 3'-5'_exonuclease_dom.
IPR020046. 5-3_exonucl_a-hlix_arch_N.
IPR020045. 5-3_exonuclease_C.
IPR002421. 5-3_exonuclease_N.
IPR019760. DNA-dir_DNA_pol_A_CS.
IPR001098. DNA-dir_DNA_pol_A_palm_dom.
IPR018320. DNA_polymerase_1.
IPR002298. DNA_polymerase_A.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF01367. 5_3_exonuc. 1 hit.
PF02739. 5_3_exonuc_N. 1 hit.
PF00476. DNA_pol_A. 1 hit.
[Graphical view]
PRINTSiPR00868. DNAPOLI.
SMARTiSM00474. 35EXOc. 1 hit.
SM00475. 53EXOc. 1 hit.
SM00279. HhH2. 1 hit.
SM00482. POLAc. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 1 hit.
SSF53098. SSF53098. 1 hit.
SSF88723. SSF88723. 1 hit.
TIGRFAMsiTIGR00593. pola. 1 hit.
PROSITEiPS00447. DNA_POLYMERASE_A. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structures of mismatch replication errors observed in a DNA polymerase."
    Johnson S.J., Beese L.S.
    Cell 116:803-816(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 299-878 IN COMPLEX WITH MAGNESIUM.
  2. "Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase."
    Hsu G.W., Kiefer J.R., Burnouf D., Becherel O.J., Fuchs R.P., Beese L.S.
    J. Biol. Chem. 279:50280-50285(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 299-878.
  3. "Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus."
    Takami H., Takaki Y., Chee G.J., Nishi S., Shimamura S., Suzuki H., Matsui S., Uchiyama I.
    Nucleic Acids Res. 32:6292-6303(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HTA426Imported.
  4. "The structural basis for the mutagenicity of O(6)-methyl-guanine lesions."
    Warren J.J., Forsberg L.J., Beese L.S.
    Proc. Natl. Acad. Sci. U.S.A. 103:19701-19706(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 300-878 IN COMPLEX WITH MAGNESIUM AND MANGANESE.
  5. "The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism."
    Wu E.Y., Beese L.S.
    J. Biol. Chem. 286:19758-19767(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.81 ANGSTROMS) OF 299-878.
  6. "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis."
    Wang W., Hellinga H.W., Beese L.S.
    Proc. Natl. Acad. Sci. U.S.A. 108:17644-17648(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.52 ANGSTROMS) OF 287-878 IN COMPLEX WITH MAGNESIUM AND MANGANESE.
  7. "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides."
    Wang W., Wu E.Y., Hellinga H.W., Beese L.S.
    J. Biol. Chem. 287:28215-28226(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS) OF 287-878 IN COMPLEX WITH CTP AND MAGNESIUM.
  8. "Structures of a High-fidelity DNA Polymerase."
    Wang W., Hellinga H.W., Beese L.S.
    Submitted (MAY-2012) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS) OF 287-878.

Entry informationi

Entry nameiQ5KWC1_GEOKA
AccessioniPrimary (citable) accession number: Q5KWC1
Entry historyi
Integrated into UniProtKB/TrEMBL: February 1, 2005
Last sequence update: February 1, 2005
Last modified: June 24, 2015
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteome, Reference proteomeImported

External Data

Dasty 3

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 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.