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Protein

DNA topoisomerase 1

Gene

topA

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.UniRule annotation

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotation

Cofactori

Mg2+UniRule annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8Magnesium 1; catalyticUniRule annotation1
Metal bindingi82Magnesium 1; catalyticUniRule annotation1
Metal bindingi82Magnesium 2UniRule annotation1
Metal bindingi84Magnesium 2UniRule annotation1
Active sitei297O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri572 – 598C4-type 1Add BLAST27
Zinc fingeri616 – 642C4-type 2Add BLAST27
Zinc fingeri663 – 689C4-type 3Add BLAST27
Zinc fingeri702 – 725C4-type 4Add BLAST24

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
LigandMagnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciHPY:HP0116-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IUniRule annotation
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topAUniRule annotation
Ordered Locus Names:HP_0116
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000000429 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451501 – 736DNA topoisomerase 1Add BLAST736

Proteomic databases

PaxDbiP55991
PRIDEiP55991

Interactioni

Subunit structurei

Monomer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei32Interaction with DNAUniRule annotation1
Sitei139Interaction with DNAUniRule annotation1
Sitei140Interaction with DNAUniRule annotation1
Sitei143Interaction with DNAUniRule annotation1
Sitei299Interaction with DNAUniRule annotation1
Sitei484Interaction with DNAUniRule annotation1

Binary interactionsi

WithEntry#Exp.IntActNotes
HP_1559O260813EBI-7493738,EBI-7500288

Protein-protein interaction databases

DIPiDIP-3057N
IntActiP55991, 16 interactors
MINTiP55991
STRINGi85962.HP0116

Structurei

3D structure databases

ProteinModelPortaliP55991
SMRiP55991
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 113ToprimUniRule annotationAdd BLAST112

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni163 – 168Interaction with DNAUniRule annotation6

Sequence similaritiesi

Belongs to the type IA topoisomerase family.UniRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri572 – 598C4-type 1Add BLAST27
Zinc fingeri616 – 642C4-type 2Add BLAST27
Zinc fingeri663 – 689C4-type 3Add BLAST27
Zinc fingeri702 – 725C4-type 4Add BLAST24

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG4105C73 Bacteria
COG0550 LUCA
COG0551 LUCA
KOiK03168
OMAiPECKYTR

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03363 TOPRIM_TopoIA_TopoI, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 2 hits
2.70.20.10, 2 hits
HAMAPiMF_00952 Topoisom_1_prok, 1 hit
InterProiView protein in InterPro
IPR003601 Topo_IA_2
IPR023406 Topo_IA_AS
IPR013497 Topo_IA_cen
IPR013824 Topo_IA_cen_sub1
IPR013825 Topo_IA_cen_sub2
IPR013826 Topo_IA_cen_sub3
IPR023405 Topo_IA_core_domain
IPR003602 Topo_IA_DNA-bd_dom
IPR013498 Topo_IA_Znf
IPR005733 TopoI_bac-type
IPR028612 Topoisom_1_IA
IPR006171 TOPRIM_domain
IPR034149 TOPRIM_TopoI
PfamiView protein in Pfam
PF01131 Topoisom_bac, 1 hit
PF01751 Toprim, 1 hit
PF01396 zf-C4_Topoisom, 3 hits
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SUPFAMiSSF56712 SSF56712, 1 hit
TIGRFAMsiTIGR01051 topA_bact, 1 hit
PROSITEiView protein in PROSITE
PS00396 TOPOISOMERASE_I_PROK, 1 hit
PS50880 TOPRIM, 1 hit

Sequencei

Sequence statusi: Complete.

P55991-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKHLIIVESP AKAKTIKNFL DKNYEVIASK GHVRDLSKFA LGIKIDETGF
60 70 80 90 100
TPNYVVDKDH KELVKQIIEL SKKASITYIA TDEDREGEAI GYHVACLIGG
110 120 130 140 150
KLESYPRIVF HEITQNAILN ALKTPRKIDM SKVNAQQARR FLDRIVGFKL
160 170 180 190 200
SSLIASKITK GLSAGRVQSA ALKLVIDKER EIKAFKPLTY FTLDAYFESH
210 220 230 240 250
LEAQLISYKG NKLKAQELID EKKAQEIKNE LEKESYAISS IVKKSKKSPT
260 270 280 290 300
PPPFMTSTLQ QSASSLLGFS PTKTMSIAQK LYEGVATPQG VMGVITYMRT
310 320 330 340 350
DSLNIAKEAL EEARNKILKD YGKDYLPPKA KVYSSKNKNA QEAHEAIRPT
360 370 380 390 400
SIILEPNALK DYLKPEELRL YTLIYKRFLA SQMQDALFES QSVVVACEKG
410 420 430 440 450
EFKASGRKLL FDGYYKILGN DDKDKLLPNL KENDPIKLEK LESNAHVTEP
460 470 480 490 500
PARYSEASLI KVLESLGIGR PSTYAPTISL LQNRDYIKVE KKQISALESA
510 520 530 540 550
FKVIEILEKH FEEIVDSKFS ASLEEELDNI AQNKADYQQV LKDFYYPFMD
560 570 580 590 600
KIEAGKKNII SQKVHEKTGQ SCPKCGGELV KKNSRYGEFI ACNNYPKCKY
610 620 630 640 650
VKQTESANDE ADQELCEKCG GEMVQKFSRN GAFLACNNYP ECKNTKSLKN
660 670 680 690 700
TPNAKETIEG VKCPECGGDI ALKRSKKGSF YGCNNYPKCN FLSNHKPINK
710 720 730
RCEKCHYLMS ERIYRKKKAH ECIKCKERVF LEEDNG
Length:736
Mass (Da):83,196
Last modified:November 1, 1997 - v1
Checksum:i357CE39735F48475
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA Translation: AAD07184.1
PIRiD64534
RefSeqiNP_206916.1, NC_000915.1
WP_000681408.1, NC_018939.1

Genome annotation databases

EnsemblBacteriaiAAD07184; AAD07184; HP_0116
GeneIDi898836
KEGGiheo:C694_00575
hpy:HP0116
PATRICifig|85962.47.peg.125

Similar proteinsi

Entry informationi

Entry nameiTOP1_HELPY
AccessioniPrimary (citable) accession number: P55991
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: May 23, 2018
This is version 123 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

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