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Q5KWC1

- Q5KWC1_GEOKA

UniProt

Q5KWC1 - Q5KWC1_GEOKA

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Protein
DNA polymerase
Gene
polA, GK2730
Organism
Geobacillus kaustophilus (strain HTA426)
Status
Unreviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei327 – 3271SucroseImported
Binding sitei410 – 4101Sucrose; via carbonyl oxygenImported
Binding sitei517 – 5171SucroseImported
Binding sitei521 – 5211SucroseImported
Binding sitei579 – 5791SucroseImported
Binding sitei609 – 6091SucroseImported
Binding sitei617 – 6171CTPImported
Binding sitei631 – 6311CTP
Metal bindingi655 – 6551MagnesiumImported
Metal bindingi655 – 6551ManganeseImported
Binding sitei655 – 6551Sulfate 6
Metal bindingi656 – 6561Magnesium; via carbonyl oxygenImported
Metal bindingi656 – 6561Manganese; via carbonyl oxygenImported
Binding sitei658 – 6581CTPImported
Binding sitei684 – 6841CTPImported
Binding sitei704 – 7041CTPImported
Binding sitei708 – 7081CTPImported
Binding sitei712 – 7121CTPImported
Binding sitei716 – 7161CTP
Binding sitei750 – 7501Sulfate 5
Binding sitei760 – 7601SucroseImported
Binding sitei786 – 7861SucroseImported
Binding sitei790 – 7901SucroseImported
Metal bindingi832 – 8321MagnesiumImported
Metal bindingi832 – 8321ManganeseImported
Binding sitei832 – 8321CTPImported
Binding sitei833 – 8331Sulfate 6

Regions

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

GO - Molecular functioni

  1. 3'-5' exonuclease activity Source: InterPro
  2. DNA binding Source: UniProtKB-KW
  3. DNA-directed DNA polymerase activity Source: UniProtKB-KW
  4. metal ion binding Source: UniProtKB-KW
  5. nucleotide binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

DNA replicationUniRule annotation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotations, MagnesiumImported, ManganeseImported, Metal-bindingImported, Nucleotide-bindingImported

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: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi235909.GK2730.

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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-ray1.60A/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.

Miscellaneous databases

EvolutionaryTraceiQ5KWC1.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni374 – 3774Sucrose bindingImported
Regioni528 – 5314Sucrose bindingImported
Regioni669 – 6713Sulfate 5 binding

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000020998.
KOiK02335.
OMAiAPMQGSA.
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

MRLKKKLVLI DGSSVAYRAF FALPLLHNDK GIHTNAVYGF TMMLNKILAE    50
EEPTHMLVAF DAGKTTFRHE AFQEYKGGRQ QTPPELSEQF PLLRELLRAY 100
RIPAYELENY EADDIIGTLA ARAEQEGFEV KVISGDRDLT QLASPHVTVD 150
ITKKGITDIE PYTPETVREK YGLTPEQIVD LKGLMGDKSD NIPGVPGIGE 200
KTAVKLLRQF GTVENVLASI DEIKGEKLKE TLRQHREMAL LSKKLAAIRR 250
DAPVELSLDD IVYQGEDREK VVALFKELGF QSFLEKMESP SSEEEKPLAK 300
MAFTLADRVT EEMLADKAAL VVEVVEENYH DAPIVGIAVV NEHGRFFLRP 350
ETALADPQFV AWLGDETKKK SMFDSKRAAV ALKWKGIELC GVSFDLLLAA 400
YLLDPAQGVD DVAAAAKMKQ YEAVRPDEAV YGKGAKRAVP DEPVLAEHLV 450
RKAAAIWELE RPFLDELRRN EQDRLLVELE QPLSSILAEM EFAGVKVDTK 500
RLEQMGKELA EQLGTVEQRI YELAGQEFNI NSPKQLGVIL FEKLQLPVLK 550
KTKTGYSTSA DVLEKLAPYH EIVENILHYR QLGKLQSTYI EGLLKVVRPD 600
TKKVHTIFNQ ALTQTGRLSS TEPNLQNIPI RLEEGRKIRQ AFVPSESDWL 650
IFAADYSQIE LRVLAHIAED DNLMEAFRRD LDIHTKTAMD IFQVSEDEVT 700
PNMRRQAKAV NFGIVYGISD YGLAQNLNIS RKEAAEFIER YFESFPGVKR 750
YMENIVQEAK QKGYVTTLLH RRRYLPDITS RNFNVRSFAE RMAMNTPIQG 800
SAADIIKKAM IDLNARLKEE RLQARLLLQV HDELILEAPK EEMERLCRLV 850
PEVMEQAVTL RVPLKVDYHY GSTWYDAK 878
Length:878
Mass (Da):99,646
Last modified:February 1, 2005 - v1
Checksum:iD50E58940CE21B01
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000043 Genomic DNA. Translation: BAD77015.1.
RefSeqiYP_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:
EMBL
GenBank
DDBJ
Links Updated
BA000043 Genomic DNA. Translation: BAD77015.1 .
RefSeqi YP_148583.1. NC_006510.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1NJW X-ray 1.90 A 299-878 [» ]
1UA0 X-ray 2.10 A 299-878 [» ]
2HHU X-ray 1.80 A 300-878 [» ]
2HHV X-ray 1.55 A 300-878 [» ]
2HHW X-ray 1.88 A/D 299-878 [» ]
2HHX X-ray 2.26 A 300-878 [» ]
2HVI X-ray 1.98 A/D 300-878 [» ]
3HP6 X-ray 1.81 A/D 299-878 [» ]
3PV8 X-ray 1.52 A/D 287-878 [» ]
3PX0 X-ray 1.73 A/D 287-878 [» ]
3PX4 X-ray 1.58 A/D 287-878 [» ]
3PX6 X-ray 1.59 A/D 287-878 [» ]
4DQI X-ray 1.69 A/D 287-878 [» ]
4DQP X-ray 1.74 A/D 287-878 [» ]
4DQQ X-ray 1.60 A/D 287-878 [» ]
4DQR X-ray 1.95 A/D 287-878 [» ]
4DQS X-ray 1.66 A 287-878 [» ]
4DS4 X-ray 1.68 A/D 287-878 [» ]
4DS5 X-ray 1.68 A/D 287-878 [» ]
4DSE X-ray 1.67 A/D 287-878 [» ]
4DSF X-ray 1.66 A/D 287-878 [» ]
4E0D X-ray 1.58 A 287-878 [» ]
4EZ6 X-ray 1.64 A/D 287-878 [» ]
4EZ9 X-ray 1.64 A/D 287-878 [» ]
4F2R X-ray 1.63 A/D 287-878 [» ]
4F2S X-ray 1.65 A/D 287-878 [» ]
4F3O X-ray 1.57 A/D 287-878 [» ]
4F4K X-ray 1.60 A/D 287-878 [» ]
4F8R X-ray 1.64 A/D 287-878 [» ]
ProteinModelPortali Q5KWC1.
SMRi Q5KWC1. Positions 299-878.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 235909.GK2730.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD77015 ; BAD77015 ; GK2730 .
GeneIDi 3184068.
KEGGi gka:GK2730.
PATRICi 21966931. VBIGeoKau81518_2914.

Phylogenomic databases

HOGENOMi HOG000020998.
KOi K02335.
OMAi APMQGSA.
OrthoDBi EOG6SJJH7.

Enzyme and pathway databases

BioCyci GKAU235909:GJO7-2825-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q5KWC1.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
3.40.50.1010. 1 hit.
InterProi IPR002562. 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 ]
Pfami PF01367. 5_3_exonuc. 1 hit.
PF02739. 5_3_exonuc_N. 1 hit.
PF00476. DNA_pol_A. 1 hit.
[Graphical view ]
PRINTSi PR00868. DNAPOLI.
SMARTi SM00474. 35EXOc. 1 hit.
SM00475. 53EXOc. 1 hit.
SM00279. HhH2. 1 hit.
SM00482. POLAc. 1 hit.
[Graphical view ]
SUPFAMi SSF47807. SSF47807. 1 hit.
SSF53098. SSF53098. 1 hit.
SSF88723. SSF88723. 1 hit.
TIGRFAMsi TIGR00593. pola. 1 hit.
PROSITEi PS00447. DNA_POLYMERASE_A. 1 hit.
[Graphical view ]
ProtoNeti Search...

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 AND SUCROSE.
  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 IN COMPLEX WITH SUCROSE.
  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; MANGANESE AND SUCROSE.
  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 IN COMPLEX WITH SUCROSE.
  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 (1.63 ANGSTROMS) OF 287-878 IN COMPLEX WITH CTP AND SUCROSE.

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: September 3, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported, Complete proteome

External Data

Dasty 3

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