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Q5KWC1 (Q5KWC1_GEOKA) Unreviewed, UniProtKB/TrEMBL

Last modified June 11, 2014. Version 88. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein namesRecommended name:
DNA polymerase RuleBase RU004460

EC=2.7.7.7 RuleBase RU004460
Gene names
Name:polA EMBL BAD77015.1
Ordered Locus Names:GK2730 EMBL BAD77015.1
OrganismGeobacillus kaustophilus (strain HTA426) [Complete proteome] [HAMAP] EMBL BAD77015.1
Taxonomic identifier235909 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Protein attributes

Sequence length878 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

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

Sequence similarities

Belongs to the DNA polymerase type-A family. RuleBase RU004459

Contains 5'-3' exonuclease domain. SAAS SAAS008918

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Nucleotide binding471 – 4755CTP PDB 4DQQ PDB 4DQS
Nucleotide binding769 – 7702CTP PDB 4DQQ PDB 4DQS
Region308 – 3114Sulfate 3 binding PDB 3HP6
Region374 – 3774Sucrose binding PDB 2HVI PDB 2HHX PDB 4F2R PDB 4F2S PDB 3HP6
Region528 – 5314Sucrose binding PDB 2HHX
Region657 – 6582Sulfate 8 binding PDB 4E0D
Region669 – 6713Sulfate 5 binding
Region781 – 7822Sulfate 15 binding PDB 3PX0 PDB 3PX6 PDB 4F3O PDB 4DQQ PDB 4DQR PDB 4EZ9 PDB 4F4K PDB 4F8R

Sites

Metal binding6551Magnesium PDB 3PV8 PDB 4DQI PDB 2HVI
Metal binding6551Manganese PDB 3PX0 PDB 2HHW PDB 3PX6
Metal binding6561Magnesium; via carbonyl oxygen PDB 3PV8 PDB 4DQI PDB 2HVI
Metal binding6561Manganese; via carbonyl oxygen PDB 3PX0 PDB 2HHW PDB 3PX6
Metal binding8321Magnesium PDB 3PV8 PDB 4DQI PDB 2HVI
Metal binding8321Manganese PDB 3PX0 PDB 2HHW PDB 3PX6
Binding site3021Sulfate 1; via amide nitrogen PDB 1UA0 PDB 2HHU PDB 2HHX
Binding site3021Sulfate 2; via amide nitrogen PDB 2HHV
Binding site3111Sulfate 4; via amide nitrogen PDB 2HHW
Binding site3261Sulfate 5 PDB 4E0D
Binding site3271Sucrose PDB 2HVI PDB 2HHX PDB 4F2R PDB 4F2S PDB 3HP6
Binding site3451Sulfate 1 PDB 2HHU PDB 2HHX
Binding site4101Sucrose; via carbonyl oxygen PDB 2HVI PDB 2HHX PDB 4F2R PDB 4F2S PDB 3HP6
Binding site5171Sucrose PDB 2HHX
Binding site5191Sulfate 6 PDB 3PV8 PDB 4DQI PDB 3PX0 PDB 4F3O PDB 4F8R
Binding site5211Sucrose PDB 2HHX
Binding site5751Sulfate 6 PDB 3PV8 PDB 4DQI PDB 3PX0 PDB 4F3O
Binding site5791Sucrose PDB 2HHX
Binding site6091Sucrose PDB 2HVI PDB 2HHX PDB 4F2R PDB 4F2S PDB 3HP6
Binding site6171CTP PDB 4DQR
Binding site6311CTP PDB 4F2R PDB 4F2S
Binding site6551Sulfate 6
Binding site6551Sulfate 7 PDB 2HHX
Binding site6581CTP PDB 4DQR PDB 4F2R PDB 4F2S
Binding site6581Sulfate 9 PDB 4F8R
Binding site6791Sulfate 10 PDB 1NJW PDB 4DQS PDB 4E0D
Binding site6841CTP PDB 4DQR PDB 4F2R PDB 4F2S
Binding site6841Sulfate 9 PDB 4F8R
Binding site7041CTP PDB 4DQR PDB 4F2R PDB 4F2S
Binding site7041Sulfate 11 PDB 2HHU PDB 2HHV PDB 2HHX
Binding site7041Sulfate 12 PDB 1NJW PDB 4DQS PDB 4E0D
Binding site7081CTP PDB 4DQR PDB 4F2R PDB 4F2S
Binding site7081Sulfate 11 PDB 2HHU PDB 2HHV PDB 2HHX
Binding site7081Sulfate 12 PDB 1NJW PDB 4DQS PDB 4E0D
Binding site7121CTP PDB 4DQR
Binding site7161CTP PDB 4F2R PDB 4F2S
Binding site7311Sulfate 14 PDB 2HHV
Binding site7501Sulfate 5
Binding site7601Sucrose PDB 2HHU PDB 2HHV
Binding site7811Sulfate 16 PDB 4E0D
Binding site7861Sucrose PDB 2HHU PDB 2HHV
Binding site7901Sucrose PDB 2HHU PDB 2HHV
Binding site8211Sulfate 17 PDB 1NJW PDB 1UA0 PDB 2HHU PDB 2HHV PDB 2HHX
Binding site8321CTP PDB 4DQR
Binding site8331Sulfate 6
Binding site8331Sulfate 7 PDB 2HHX

Sequences

Sequence LengthMass (Da)Tools
Q5KWC1 [UniParc].

Last modified February 1, 2005. Version 1.
Checksum: D50E58940CE21B01

FASTA87899,646
        10         20         30         40         50         60 
MRLKKKLVLI DGSSVAYRAF FALPLLHNDK GIHTNAVYGF TMMLNKILAE EEPTHMLVAF 

        70         80         90        100        110        120 
DAGKTTFRHE AFQEYKGGRQ QTPPELSEQF PLLRELLRAY RIPAYELENY EADDIIGTLA 

       130        140        150        160        170        180 
ARAEQEGFEV KVISGDRDLT QLASPHVTVD ITKKGITDIE PYTPETVREK YGLTPEQIVD 

       190        200        210        220        230        240 
LKGLMGDKSD NIPGVPGIGE KTAVKLLRQF GTVENVLASI DEIKGEKLKE TLRQHREMAL 

       250        260        270        280        290        300 
LSKKLAAIRR DAPVELSLDD IVYQGEDREK VVALFKELGF QSFLEKMESP SSEEEKPLAK 

       310        320        330        340        350        360 
MAFTLADRVT EEMLADKAAL VVEVVEENYH DAPIVGIAVV NEHGRFFLRP ETALADPQFV 

       370        380        390        400        410        420 
AWLGDETKKK SMFDSKRAAV ALKWKGIELC GVSFDLLLAA YLLDPAQGVD DVAAAAKMKQ 

       430        440        450        460        470        480 
YEAVRPDEAV YGKGAKRAVP DEPVLAEHLV RKAAAIWELE RPFLDELRRN EQDRLLVELE 

       490        500        510        520        530        540 
QPLSSILAEM EFAGVKVDTK RLEQMGKELA EQLGTVEQRI YELAGQEFNI NSPKQLGVIL 

       550        560        570        580        590        600 
FEKLQLPVLK KTKTGYSTSA DVLEKLAPYH EIVENILHYR QLGKLQSTYI EGLLKVVRPD 

       610        620        630        640        650        660 
TKKVHTIFNQ ALTQTGRLSS TEPNLQNIPI RLEEGRKIRQ AFVPSESDWL IFAADYSQIE 

       670        680        690        700        710        720 
LRVLAHIAED DNLMEAFRRD LDIHTKTAMD IFQVSEDEVT PNMRRQAKAV NFGIVYGISD 

       730        740        750        760        770        780 
YGLAQNLNIS RKEAAEFIER YFESFPGVKR YMENIVQEAK QKGYVTTLLH RRRYLPDITS 

       790        800        810        820        830        840 
RNFNVRSFAE RMAMNTPIQG SAADIIKKAM IDLNARLKEE RLQARLLLQV HDELILEAPK 

       850        860        870 
EEMERLCRLV PEVMEQAVTL RVPLKVDYHY GSTWYDAK 

« Hide

References

« Hide 'large scale' references
[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; SUCROSE AND SULFATE.
[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 AND SULFATE.
[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: HTA426 EMBL BAD77015.1.
[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; SUCROSE AND SULFATE.
[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 AND SULFATE.
[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; MANGANESE AND SULFATE.
[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; MAGNESIUM AND SULFATE.
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BA000043 Genomic DNA. Translation: BAD77015.1.
RefSeqYP_148583.1. NC_006510.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalQ5KWC1.
SMRQ5KWC1. Positions 299-878.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING235909.GK2730.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD77015; BAD77015; GK2730.
GeneID3184068.
KEGGgka:GK2730.
PATRIC21966931. VBIGeoKau81518_2914.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHOG000020998.
KOK02335.
OMAAPMQGSA.
OrthoDBEOG6SJJH7.

Enzyme and pathway databases

BioCycGKAU235909:GJO7-2825-MONOMER.

Family and domain databases

Gene3D3.30.420.10. 1 hit.
3.40.50.1010. 1 hit.
InterProIPR002562. 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]
PfamPF01367. 5_3_exonuc. 1 hit.
PF02739. 5_3_exonuc_N. 1 hit.
PF00476. DNA_pol_A. 1 hit.
[Graphical view]
PRINTSPR00868. DNAPOLI.
SMARTSM00474. 35EXOc. 1 hit.
SM00475. 53EXOc. 1 hit.
SM00279. HhH2. 1 hit.
SM00482. POLAc. 1 hit.
[Graphical view]
SUPFAMSSF47807. SSF47807. 1 hit.
SSF53098. SSF53098. 1 hit.
SSF88723. SSF88723. 1 hit.
TIGRFAMsTIGR00593. pola. 1 hit.
PROSITEPS00447. DNA_POLYMERASE_A. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ5KWC1.

Entry information

Entry nameQ5KWC1_GEOKA
AccessionPrimary (citable) accession number: Q5KWC1
Entry history
Integrated into UniProtKB/TrEMBL: February 1, 2005
Last sequence update: February 1, 2005
Last modified: June 11, 2014
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)