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Protein

DNA polymerase I

Gene

polA

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.

Catalytic activityi

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

Temperature dependencei

Optimum temperature is 65 degrees Celsius.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase I (EC:2.7.7.7)
Short name:
POL I
Gene namesi
Name:polA
Synonyms:pol
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi73 – 731Y → A or P: Complete loss of 5'-3' exonuclease activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 876876DNA polymerase IPRO_0000101234Add
BLAST

Interactioni

Subunit structurei

Single-chain monomer with multiple functions.

Structurei

Secondary structure

1
876
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi302 – 3065Combined sources
Helixi309 – 3124Combined sources
Beta strandi314 – 3218Combined sources
Beta strandi324 – 3263Combined sources
Beta strandi334 – 3396Combined sources
Beta strandi342 – 3465Combined sources
Helixi348 – 3514Combined sources
Helixi355 – 3628Combined sources
Beta strandi366 – 3727Combined sources
Helixi373 – 3819Combined sources
Turni382 – 3843Combined sources
Beta strandi390 – 3934Combined sources
Helixi394 – 4018Combined sources
Helixi403 – 4053Combined sources
Helixi410 – 4156Combined sources
Turni416 – 4183Combined sources
Helixi425 – 4295Combined sources
Helixi432 – 4343Combined sources
Helixi440 – 46728Combined sources
Helixi471 – 4766Combined sources
Helixi478 – 49114Combined sources
Beta strandi493 – 4953Combined sources
Helixi497 – 52226Combined sources
Helixi531 – 5399Combined sources
Beta strandi548 – 5503Combined sources
Beta strandi551 – 5544Combined sources
Helixi558 – 5647Combined sources
Helixi565 – 5673Combined sources
Helixi570 – 58718Combined sources
Helixi589 – 5946Combined sources
Turni597 – 5993Combined sources
Beta strandi605 – 6095Combined sources
Beta strandi612 – 6143Combined sources
Beta strandi617 – 6215Combined sources
Helixi623 – 6253Combined sources
Beta strandi628 – 6303Combined sources
Helixi631 – 6344Combined sources
Helixi635 – 6395Combined sources
Beta strandi647 – 65610Combined sources
Helixi657 – 66610Combined sources
Helixi669 – 6768Combined sources
Helixi681 – 6899Combined sources
Helixi694 – 6963Combined sources
Helixi699 – 71416Combined sources
Helixi718 – 7258Combined sources
Helixi729 – 74214Combined sources
Helixi744 – 76017Combined sources
Beta strandi761 – 7644Combined sources
Beta strandi770 – 7723Combined sources
Helixi774 – 7774Combined sources
Helixi781 – 81737Combined sources
Beta strandi823 – 8275Combined sources
Beta strandi829 – 8379Combined sources
Helixi838 – 8403Combined sources
Helixi841 – 85313Combined sources
Beta strandi864 – 8718Combined sources
Turni872 – 8743Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L3SX-ray1.70A301-876[»]
1L3TX-ray1.70A301-876[»]
1L3UX-ray1.80A301-876[»]
1L3VX-ray1.71A301-876[»]
1L5UX-ray1.95A301-876[»]
1LV5X-ray1.95A/B301-876[»]
1NJXX-ray1.65A301-876[»]
1NJYX-ray2.00A301-876[»]
1NJZX-ray2.00A301-876[»]
1NK0X-ray1.70A301-876[»]
1NK4X-ray1.60A301-876[»]
1NK5X-ray2.10A301-876[»]
1NK6X-ray2.10A301-876[»]
1NK7X-ray1.90A301-876[»]
1NK8X-ray1.90A301-876[»]
1NK9X-ray1.90A301-876[»]
1NKBX-ray2.00A301-876[»]
1NKCX-ray1.80A301-876[»]
1NKEX-ray1.80A301-876[»]
1U45X-ray2.01A301-876[»]
1U47X-ray2.00A301-876[»]
1U48X-ray2.10A301-876[»]
1U49X-ray2.15A301-876[»]
1U4BX-ray1.60A301-876[»]
1UA1X-ray2.00A301-876[»]
1XC9X-ray1.90A301-876[»]
1XWLX-ray1.70A297-876[»]
2BDPX-ray1.80A297-876[»]
3BDPX-ray1.90A297-876[»]
3EYZX-ray2.10A304-876[»]
3EZ5X-ray1.90A/D304-876[»]
4BDPX-ray1.80A297-876[»]
ProteinModelPortaliP52026.
SMRiP52026. Positions 299-876.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP52026.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 3103105'-3' exonucleaseAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni289 – 876588Subtilisin large fragmentAdd
BLAST
Regioni469 – 876408PolymeraseAdd
BLAST

Sequence similaritiesi

Belongs to the DNA polymerase type-A family.Curated
Contains 1 3'-5' exonuclease domain.Curated
Contains 1 5'-3' exonuclease domain.Curated

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.

P52026-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKNKLVLIDG NSVAYRAFFA LPLLHNDKGI HTNAVYGFTM MLNKILAEEQ
60 70 80 90 100
PTHILVAFDA GKTTFRHETF QDYKGGRQQT PPELSEQFPL LRELLKAYRI
110 120 130 140 150
PAYELDHYEA DDIIGTMAAR AEREGFAVKV ISGDRDLTQL ASPQVTVEIT
160 170 180 190 200
KKGITDIESY TPETVVEKYG LTPEQIVDLK GLMGDKSDNI PGVPGIGEKT
210 220 230 240 250
AVKLLKQFGT VENVLASIDE IKGEKLKENL RQYRDLALLS KQLAAICRDA
260 270 280 290 300
PVELTLDDIV YKGEDREKVV ALFQELGFQS FLDKMAVQTD EGEKPLAGMD
310 320 330 340 350
FAIADSVTDE MLADKAALVV EVVGDNYHHA PIVGIALANE RGRFFLRPET
360 370 380 390 400
ALADPKFLAW LGDETKKKTM FDSKRAAVAL KWKGIELRGV VFDLLLAAYL
410 420 430 440 450
LDPAQAAGDV AAVAKMHQYE AVRSDEAVYG KGAKRTVPDE PTLAEHLVRK
460 470 480 490 500
AAAIWALEEP LMDELRRNEQ DRLLTELEQP LAGILANMEF TGVKVDTKRL
510 520 530 540 550
EQMGAELTEQ LQAVERRIYE LAGQEFNINS PKQLGTVLFD KLQLPVLKKT
560 570 580 590 600
KTGYSTSADV LEKLAPHHEI VEHILHYRQL GKLQSTYIEG LLKVVHPVTG
610 620 630 640 650
KVHTMFNQAL TQTGRLSSVE PNLQNIPIRL EEGRKIRQAF VPSEPDWLIF
660 670 680 690 700
AADYSQIELR VLAHIAEDDN LIEAFRRGLD IHTKTAMDIF HVSEEDVTAN
710 720 730 740 750
MRRQAKAVNF GIVYGISDYG LAQNLNITRK EAAEFIERYF ASFPGVKQYM
760 770 780 790 800
DNIVQEAKQK GYVTTLLHRR RYLPDITSRN FNVRSFAERT AMNTPIQGSA
810 820 830 840 850
ADIIKKAMID LSVRLREERL QARLLLQVHD ELILEAPKEE IERLCRLVPE
860 870
VMEQAVTLRV PLKVDYHYGP TWYDAK
Length:876
Mass (Da):98,670
Last modified:July 15, 1998 - v2
Checksum:i689167A801D543E4
GO

Sequence cautioni

The sequence AAA85558.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti91 – 911L → V in AAA85558 (PubMed:8679703).Curated
Sequence conflicti198 – 1981E → K in AAA85558 (PubMed:8679703).Curated
Sequence conflicti352 – 3521L → V in AAA85558 (PubMed:8679703).Curated
Sequence conflicti381 – 3822KW → NG in AAA85558 (PubMed:8679703).Curated
Sequence conflicti388 – 3881R → AGV in AAA85558 (PubMed:8679703).Curated
Sequence conflicti446 – 4461H → Q in AAA85558 (PubMed:8679703).Curated
Sequence conflicti448 – 4481V → A in AAC37139 (PubMed:7557480).Curated
Sequence conflicti479 – 4802QP → HA in AAA85558 (PubMed:8679703).Curated
Sequence conflicti678 – 6781G → W in AAA85558 (PubMed:8679703).Curated
Sequence conflicti785 – 7851S → T in AAA85558 (PubMed:8679703).Curated
Sequence conflicti814 – 8152RL → SV in AAA85558 (PubMed:8679703).Curated
Sequence conflicti828 – 8281V → G in AAA85558 (PubMed:8679703).Curated
Sequence conflicti842 – 8421E → G in AAA85558 (PubMed:8679703).Curated
Sequence conflicti857 – 8571T → A in AAC37139 (PubMed:7557480).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti298 – 2981G → K in strain: X.
Natural varianti300 – 3001D → A in strain: X.
Natural varianti302 – 3032AI → TL in strain: X.
Natural varianti306 – 3061S → R in strain: X.
Natural varianti309 – 3091D → E in strain: X.
Natural varianti320 – 3201V → L in strain: X.
Natural varianti324 – 3252GD → EE in strain: X.
Natural varianti329 – 3291H → D in strain: X.
Natural varianti337 – 3382LA → VV in strain: X.
Natural varianti341 – 3411R → H in strain: X.
Natural varianti356 – 3561K → Q in strain: X.
Natural varianti358 – 3581L → V in strain: X.
Natural varianti369 – 3691T → S in strain: X.
Natural varianti388 – 3881R → C in strain: X.
Natural varianti391 – 3911V → S in strain: X.
Natural varianti406 – 4083AAG → GVD in strain: X.
Natural varianti411 – 4111A → R in strain: X.
Natural varianti413 – 4131V → A in strain: X.
Natural varianti417 – 4171H → K in strain: X.
Natural varianti424 – 4241S → P in strain: X.
Natural varianti436 – 4361T → A in strain: X.
Natural varianti442 – 4421T → V in strain: X.
Natural varianti456 – 4561A → E in strain: X.
Natural varianti459 – 4591E → R in strain: X.
Natural varianti461 – 4622LM → FL in strain: X.
Natural varianti475 – 4751T → V in strain: X.
Natural varianti482 – 4832AG → SS in strain: X.
Natural varianti487 – 4871N → E in strain: X.
Natural varianti491 – 4911T → A in strain: X.
Natural varianti505 – 5051A → K in strain: X.
Natural varianti508 – 5081T → R in strain: X.
Natural varianti510 – 5101Q → K in strain: X.
Natural varianti512 – 5132QA → GT in strain: X.
Natural varianti516 – 5161R → Q in strain: X.
Natural varianti536 – 5372TV → VI in strain: X.
Natural varianti540 – 5401D → E in strain: X.
Natural varianti567 – 5671H → Y in strain: X.
Natural varianti573 – 5731H → N in strain: X.
Natural varianti596 – 5961H → R in strain: X.
Natural varianti598 – 5981V → D in strain: X.
Natural varianti600 – 6001G → K in strain: X.
Natural varianti605 – 6051M → I in strain: X.
Natural varianti619 – 6191V → T in strain: X.
Natural varianti645 – 6451P → S in strain: X.
Natural varianti672 – 6721I → M in strain: X.
Natural varianti678 – 6781G → D in strain: X.
Natural varianti691 – 6911H → Q in strain: X.
Natural varianti695 – 6962ED → DE in strain: X.
Natural varianti699 – 6991A → P in strain: X.
Natural varianti728 – 7281T → S in strain: X.
Natural varianti741 – 7411A → E in strain: X.
Natural varianti748 – 7481Q → R in strain: X.
Natural varianti751 – 7511D → E in strain: X.
Natural varianti790 – 7901T → M in strain: X.
Natural varianti812 – 8132SV → NA in strain: X.
Natural varianti816 – 8161R → K in strain: X.
Natural varianti841 – 8411I → M in strain: X.
Natural varianti870 – 8701P → S in strain: X.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U23149 Genomic DNA. Translation: AAA85558.1. Different initiation.
L42111 Genomic DNA. Translation: AAC37139.1.
PIRiJC4286.
S70368.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U23149 Genomic DNA. Translation: AAA85558.1. Different initiation.
L42111 Genomic DNA. Translation: AAC37139.1.
PIRiJC4286.
S70368.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L3SX-ray1.70A301-876[»]
1L3TX-ray1.70A301-876[»]
1L3UX-ray1.80A301-876[»]
1L3VX-ray1.71A301-876[»]
1L5UX-ray1.95A301-876[»]
1LV5X-ray1.95A/B301-876[»]
1NJXX-ray1.65A301-876[»]
1NJYX-ray2.00A301-876[»]
1NJZX-ray2.00A301-876[»]
1NK0X-ray1.70A301-876[»]
1NK4X-ray1.60A301-876[»]
1NK5X-ray2.10A301-876[»]
1NK6X-ray2.10A301-876[»]
1NK7X-ray1.90A301-876[»]
1NK8X-ray1.90A301-876[»]
1NK9X-ray1.90A301-876[»]
1NKBX-ray2.00A301-876[»]
1NKCX-ray1.80A301-876[»]
1NKEX-ray1.80A301-876[»]
1U45X-ray2.01A301-876[»]
1U47X-ray2.00A301-876[»]
1U48X-ray2.10A301-876[»]
1U49X-ray2.15A301-876[»]
1U4BX-ray1.60A301-876[»]
1UA1X-ray2.00A301-876[»]
1XC9X-ray1.90A301-876[»]
1XWLX-ray1.70A297-876[»]
2BDPX-ray1.80A297-876[»]
3BDPX-ray1.90A297-876[»]
3EYZX-ray2.10A304-876[»]
3EZ5X-ray1.90A/D304-876[»]
4BDPX-ray1.80A297-876[»]
ProteinModelPortaliP52026.
SMRiP52026. Positions 299-876.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP52026.

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

  1. "Cloning and complete sequence of the DNA polymerase-encoding gene (BstpolI) and characterisation of the Klenow-like fragment from Bacillus stearothermophilus."
    Phang S.M., Teo C.Y., Lo E., Wong V.W.
    Gene 163:65-68(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Construction of single amino acid substitution mutants of cloned Bacillus stearothermophilus DNA polymerase I which lack 5'-3' exonuclease activity."
    Riggs M.G., Tudor S., Sivaram M., McDonough S.H.
    Biochim. Biophys. Acta 1307:178-186(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-5 AND 289-293, CHARACTERIZATION, MUTAGENESIS TO REMOVE 5'-3' EXONUCLEASE ACTIVITY.
    Strain: ATCC 12980 / DSM 22 / JCM 2501 / NBRC 12550 / NCIMB 8923 / NCTC 10339 / VKM B-510.
  3. "Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1-A resolution."
    Kiefer J.R., Mao C., Hansen C.J., Basehore S.L., Hogrefe H.H., Braman J.C., Beese L.S.
    Structure 5:95-108(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 297-876.
    Strain: X.
  4. "Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal."
    Kiefer J.R., Mao C., Braman J.C., Beese L.S.
    Nature 391:304-307(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 297-876.
    Strain: X.

Entry informationi

Entry nameiDPO1_GEOSE
AccessioniPrimary (citable) accession number: P52026
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: July 15, 1998
Last modified: May 11, 2016
This is version 110 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The enzyme from this organism does not have any 3'-5' exonuclease activity. The subtilisin large fragment (residues 289-876) has wild-type polymerase activity but no 5'-3' exonuclease activity.

Caution

PubMed:9016716 and PubMed:9440698 strain is not known and has been termed 'X' in this entry.Curated

Keywords - Technical termi

3D-structure, Direct protein sequencing

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.