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Protein

DNA topoisomerase 1

Gene

topA

Organism
Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi9 – 91Magnesium 1; catalyticUniRule annotation
Sitei33 – 331Interaction with DNAUniRule annotation
Metal bindingi82 – 821Magnesium 1; catalyticUniRule annotation
Metal bindingi82 – 821Magnesium 2UniRule annotation
Metal bindingi84 – 841Magnesium 2UniRule annotation
Sitei139 – 1391Interaction with DNAUniRule annotation
Sitei140 – 1401Interaction with DNAUniRule annotation
Sitei143 – 1431Interaction with DNAUniRule annotation
Sitei148 – 1481Interaction with DNAUniRule annotation
Sitei155 – 1551Interaction with DNAUniRule annotation
Active sitei298 – 2981O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei300 – 3001Interaction with DNAUniRule annotation
Sitei487 – 4871Interaction with DNAUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri576 – 60227C4-type 1Add
BLAST
Zinc fingeri616 – 64429C4-type 2Add
BLAST
Zinc fingeri657 – 68024C4-type 3Add
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciSSAP342451:GKFA-1577-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:SSP1518
OrganismiStaphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229)
Taxonomic identifieri342451 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus
ProteomesiUP000006371 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 688688DNA topoisomerase 1PRO_0000285947Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi342451.SSP1518.

Structurei

3D structure databases

ProteinModelPortaliQ49X35.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 113111ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni163 – 1686Interaction with DNAUniRule annotation

Sequence similaritiesi

Belongs to the type IA topoisomerase family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri576 – 60227C4-type 1Add
BLAST
Zinc fingeri616 – 64429C4-type 2Add
BLAST
Zinc fingeri657 – 68024C4-type 3Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000004018.
KOiK03168.
OMAiVVECDKC.
OrthoDBiEOG6S7XQ9.

Family and domain databases

Gene3Di1.10.460.10. 3 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
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.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q49X35-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAENLVIVES PAKAKTIEKY LGKKYKVIAS MGHVRDLPRS QMGVDAENDY
60 70 80 90 100
EPKYITIRGK GPVVKELKKH AKKAKKVFLA SDPDREGEAI AWHLANILNL
110 120 130 140 150
EDSTENRVVF NEITKDAVKD SFKHPRGIEM ELVDAQQARR ILDRLVGYNI
160 170 180 190 200
SPVLWKKVKK GLSAGRVQSV ALRLVIDREN EIRNFKPEEY WKIEGEFRYK
210 220 230 240 250
KTKFTAKFLH FKNKPFKLTE KADVEKITTQ LDGDQFEVTK VTKKEKTRYP
260 270 280 290 300
ANPFTTSTLQ QEAARKLNFK ARKTMMLAQQ LYEGIDLKKQ GTVGLITYMR
310 320 330 340 350
TDSTRISDQA QSEAKNYIQE TYGNDYTSNR KSKGQGDQDA HEAIRPSSTL
360 370 380 390 400
RTPNEMKNFL TRDQHRLYKL IWERFVASQM APAILDTVAM DLTQNDIKFR
410 420 430 440 450
ANGQTIKFKG FMTLYVETKD DSEDGKDNKL PNIGEGEMVT ATNIEPSQHF
460 470 480 490 500
TQPPPRYTEA RLVKTMEELK IGRPSTYAPT IDTIQKRNYV KNESKRFVPT
510 520 530 540 550
ELGEIVHEQV KDYFPEIIDV DFTVNMETLL DKVADGEIGW KKVISDFYSS
560 570 580 590 600
FKQDVERAEE EMEKIEIKDE PAGEDCEVCG SPMVIKMGRY GKFMACSNFP
610 620 630 640 650
DCRNTKAIVK TIGVTCPKCK EGDVVERKSK KNRIFYGCSK YPECDFVTWD
660 670 680
KPIGRDCPKC EHYLVEKKQG RKSQVVCSNC DYKEEEQK
Length:688
Mass (Da):79,130
Last modified:September 13, 2005 - v1
Checksum:i24BC79B6DD63D72B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008934 Genomic DNA. Translation: BAE18663.1.
RefSeqiWP_011303268.1. NC_007350.1.

Genome annotation databases

EnsemblBacteriaiBAE18663; BAE18663; SSP1518.
GeneIDi23779955.
KEGGissp:SSP1518.
PATRICi19624626. VBIStaSap90642_1520.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008934 Genomic DNA. Translation: BAE18663.1.
RefSeqiWP_011303268.1. NC_007350.1.

3D structure databases

ProteinModelPortaliQ49X35.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi342451.SSP1518.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAE18663; BAE18663; SSP1518.
GeneIDi23779955.
KEGGissp:SSP1518.
PATRICi19624626. VBIStaSap90642_1520.

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000004018.
KOiK03168.
OMAiVVECDKC.
OrthoDBiEOG6S7XQ9.

Enzyme and pathway databases

BioCyciSSAP342451:GKFA-1577-MONOMER.

Family and domain databases

Gene3Di1.10.460.10. 3 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
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.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection."
    Kuroda M., Yamashita A., Hirakawa H., Kumano M., Morikawa K., Higashide M., Maruyama A., Inose Y., Matoba K., Toh H., Kuhara S., Hattori M., Ohta T.
    Proc. Natl. Acad. Sci. U.S.A. 102:13272-13277(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 15305 / DSM 20229.

Entry informationi

Entry nameiTOP1_STAS1
AccessioniPrimary (citable) accession number: Q49X35
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: September 13, 2005
Last modified: July 22, 2015
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.