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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)DescriptionActionsGraphical viewLength
Mutagenesisi73Y → A or P: Complete loss of 5'-3' exonuclease activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001012341 – 876DNA polymerase IAdd BLAST876

Interactioni

Subunit structurei

Single-chain monomer with multiple functions.

Structurei

Secondary structure

1876
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi302 – 306Combined sources5
Helixi309 – 312Combined sources4
Beta strandi314 – 321Combined sources8
Beta strandi324 – 326Combined sources3
Beta strandi334 – 339Combined sources6
Beta strandi342 – 346Combined sources5
Helixi348 – 351Combined sources4
Helixi355 – 362Combined sources8
Beta strandi366 – 372Combined sources7
Helixi373 – 381Combined sources9
Turni382 – 384Combined sources3
Beta strandi390 – 393Combined sources4
Helixi394 – 401Combined sources8
Helixi403 – 405Combined sources3
Helixi410 – 415Combined sources6
Turni416 – 418Combined sources3
Helixi425 – 429Combined sources5
Helixi432 – 434Combined sources3
Helixi440 – 467Combined sources28
Helixi471 – 476Combined sources6
Helixi478 – 491Combined sources14
Beta strandi493 – 495Combined sources3
Helixi497 – 522Combined sources26
Helixi531 – 539Combined sources9
Beta strandi548 – 550Combined sources3
Beta strandi551 – 554Combined sources4
Helixi558 – 564Combined sources7
Helixi565 – 567Combined sources3
Helixi570 – 587Combined sources18
Helixi589 – 594Combined sources6
Turni597 – 599Combined sources3
Beta strandi605 – 609Combined sources5
Beta strandi612 – 614Combined sources3
Beta strandi617 – 621Combined sources5
Helixi623 – 625Combined sources3
Beta strandi628 – 630Combined sources3
Helixi631 – 634Combined sources4
Helixi635 – 639Combined sources5
Beta strandi647 – 656Combined sources10
Helixi657 – 666Combined sources10
Helixi669 – 676Combined sources8
Helixi681 – 689Combined sources9
Helixi694 – 696Combined sources3
Helixi699 – 714Combined sources16
Helixi718 – 725Combined sources8
Helixi729 – 742Combined sources14
Helixi744 – 760Combined sources17
Beta strandi761 – 764Combined sources4
Beta strandi770 – 772Combined sources3
Helixi774 – 777Combined sources4
Helixi781 – 817Combined sources37
Beta strandi823 – 827Combined sources5
Beta strandi829 – 837Combined sources9
Helixi838 – 840Combined sources3
Helixi841 – 853Combined sources13
Beta strandi864 – 871Combined sources8
Turni872 – 874Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP52026.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 3105'-3' exonucleaseAdd BLAST310

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni289 – 876Subtilisin large fragmentAdd BLAST588
Regioni469 – 876PolymeraseAdd BLAST408

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 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti91L → V in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti198E → K in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti352L → V in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti381 – 382KW → NG in AAA85558 (PubMed:8679703).Curated2
Sequence conflicti388R → AGV in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti446H → Q in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti448V → A in AAC37139 (PubMed:7557480).Curated1
Sequence conflicti479 – 480QP → HA in AAA85558 (PubMed:8679703).Curated2
Sequence conflicti678G → W in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti785S → T in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti814 – 815RL → SV in AAA85558 (PubMed:8679703).Curated2
Sequence conflicti828V → G in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti842E → G in AAA85558 (PubMed:8679703).Curated1
Sequence conflicti857T → A in AAC37139 (PubMed:7557480).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti298G → K in strain: X. 1
Natural varianti300D → A in strain: X. 1
Natural varianti302 – 303AI → TL in strain: X. 2
Natural varianti306S → R in strain: X. 1
Natural varianti309D → E in strain: X. 1
Natural varianti320V → L in strain: X. 1
Natural varianti324 – 325GD → EE in strain: X. 2
Natural varianti329H → D in strain: X. 1
Natural varianti337 – 338LA → VV in strain: X. 2
Natural varianti341R → H in strain: X. 1
Natural varianti356K → Q in strain: X. 1
Natural varianti358L → V in strain: X. 1
Natural varianti369T → S in strain: X. 1
Natural varianti388R → C in strain: X. 1
Natural varianti391V → S in strain: X. 1
Natural varianti406 – 408AAG → GVD in strain: X. 3
Natural varianti411A → R in strain: X. 1
Natural varianti413V → A in strain: X. 1
Natural varianti417H → K in strain: X. 1
Natural varianti424S → P in strain: X. 1
Natural varianti436T → A in strain: X. 1
Natural varianti442T → V in strain: X. 1
Natural varianti456A → E in strain: X. 1
Natural varianti459E → R in strain: X. 1
Natural varianti461 – 462LM → FL in strain: X. 2
Natural varianti475T → V in strain: X. 1
Natural varianti482 – 483AG → SS in strain: X. 2
Natural varianti487N → E in strain: X. 1
Natural varianti491T → A in strain: X. 1
Natural varianti505A → K in strain: X. 1
Natural varianti508T → R in strain: X. 1
Natural varianti510Q → K in strain: X. 1
Natural varianti512 – 513QA → GT in strain: X. 2
Natural varianti516R → Q in strain: X. 1
Natural varianti536 – 537TV → VI in strain: X. 2
Natural varianti540D → E in strain: X. 1
Natural varianti567H → Y in strain: X. 1
Natural varianti573H → N in strain: X. 1
Natural varianti596H → R in strain: X. 1
Natural varianti598V → D in strain: X. 1
Natural varianti600G → K in strain: X. 1
Natural varianti605M → I in strain: X. 1
Natural varianti619V → T in strain: X. 1
Natural varianti645P → S in strain: X. 1
Natural varianti672I → M in strain: X. 1
Natural varianti678G → D in strain: X. 1
Natural varianti691H → Q in strain: X. 1
Natural varianti695 – 696ED → DE in strain: X. 2
Natural varianti699A → P in strain: X. 1
Natural varianti728T → S in strain: X. 1
Natural varianti741A → E in strain: X. 1
Natural varianti748Q → R in strain: X. 1
Natural varianti751D → E in strain: X. 1
Natural varianti790T → M in strain: X. 1
Natural varianti812 – 813SV → NA in strain: X. 2
Natural varianti816R → K in strain: X. 1
Natural varianti841I → M in strain: X. 1
Natural varianti870P → S in strain: X. 1

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
PDB 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.
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...

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: November 2, 2016
This is version 112 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.