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Protein

DNA topoisomerase 1

Gene

topA

Organism
Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
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)DescriptionActionsGraphical viewLength
Metal bindingi7Magnesium 1; catalyticUniRule annotation1
Metal bindingi80Magnesium 1; catalyticUniRule annotation1
Metal bindingi80Magnesium 2UniRule annotation1
Metal bindingi82Magnesium 2UniRule annotation1
Active sitei293O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri592 – 619C4-typeAdd BLAST28

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

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:ZMO1193
OrganismiZymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
Taxonomic identifieri264203 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeZymomonas
Proteomesi
  • UP000001173 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451751 – 1212DNA topoisomerase 1Add BLAST1212

Interactioni

Subunit structurei

Monomer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei31Interaction with DNAUniRule annotation1
Sitei140Interaction with DNAUniRule annotation1
Sitei141Interaction with DNAUniRule annotation1
Sitei144Interaction with DNAUniRule annotation1
Sitei156Interaction with DNAUniRule annotation1
Sitei295Interaction with DNAUniRule annotation1
Sitei488Interaction with DNAUniRule annotation1

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 114ToprimUniRule annotationAdd BLAST114

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni164 – 169Interaction with DNAUniRule annotation6

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1109 – 1207Lys-richAdd BLAST99

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri592 – 619C4-typeAdd BLAST28

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000004020.
KOiK03168.
OMAiFRSAEYW.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 3 hits.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9X3X7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLVVVESPA KAKTIEKYLG SGYQVLASYG HIRDLPSKDG SVNPDNGFSM
60 70 80 90 100
VWQNYPDKAH RLKAIEDAVK ESDSLILATD PDREGEAISW HILELLKTKK
110 120 130 140 150
LLPDDVERVT FNAITKAAVT DAMAHPRQLD NDLINAYLAR RALDYLVGFT
160 170 180 190 200
LSPILWRKLP GAKSAGRVQS VALRLVVDRE QEIEGFKPQE YWSVEADMEA
210 220 230 240 250
DSIGFTSRLI QWRGQKLEKL SIADKTQAEA AQSDVESGHF TVSNVETKPV
260 270 280 290 300
SRNPQPPFTT STLQQEAARK LGFAASHTMR LAQSLYEEGL ITYMRTDGVQ
310 320 330 340 350
MDESAIAAAR KTITQRYDGG YVPDKPRQYQ VKAKNAQEAH EAIRPTDFSR
360 370 380 390 400
DKAASGDHAR LYELIWKRAL ASQMASAKLE RTTVDLTDGT GQNVLRVTGQ
410 420 430 440 450
VVLFSGFLTL YEESADDNAN DRDGKEGRAR LPLLRAGDAP LKKEVRADQH
460 470 480 490 500
FTQPPPRYSE ASLVKKMEDL GIGRPSTYAS VIQVLKDRAY VTLERNRFIP
510 520 530 540 550
SEAGRLLTAF LERFFERYVS YDFTAGLEDS LDEISGGRAD WQKVLDAFWH
560 570 580 590 600
DFKPKTAEVM EQQPSAITAE LDKFLEPWLF PDKGDGHDPR ECPSCHTGRL
610 620 630 640 650
ALKGGRFGAF IACSNYPECK YTRGFGQGED GVDDNEPVLL GYMPENSDDD
660 670 680 690 700
GYMAFSDQGD ILPANTASAS ETGVTDGGIA ANAAFSGKGN SASHTDRDDL
710 720 730 740 750
PFDPDEPASS TGNVASSQSR MTGDETASSG NSRDSSAHGV STTAGIDAES
760 770 780 790 800
QAGISNQALA GKNNAGRTAV SDNKGNNSSS TIAAARKGGS TDDNATVSDP
810 820 830 840 850
DGDIGSGASS SGQDADNRLL SHRNGDIDSR AIPADHKDSS SDQNASHALS
860 870 880 890 900
PDRNSDDASV SNSDKKIDSK AVSTGHDVGN AITSDNSPSD NVAHLASTPS
910 920 930 940 950
SATSSVKVAL ETENNDTAAS KADEQAKEEE ESRKARAVTR RTGRFGPYIQ
960 970 980 990 1000
LGEGKNAKRV SVPRDVNPRE VDFSLASRLL ALPREIGLHP ESGKMIIAGT
1010 1020 1030 1040 1050
GRYGPYLNCD GKYARLSSTE ELLDIDIDRA VVKLAEAAQN KGRTGATLSR
1060 1070 1080 1090 1100
EPLKVFGDSP VTEKPVQLMN GRYGPYVTDG ETNASLPKDT TPESLTFEEA
1110 1120 1130 1140 1150
LALLEARAKM PKKKKTKKAA AKKPAAKKTT TKKAAPKKAT TKTATPKSAT
1160 1170 1180 1190 1200
TDNATSEDGD ATPAKSPAKK AVAKKTTAKK PASKSATKKA PSSKTTAAKK
1210
TSKATPKDEV AE
Length:1,212
Mass (Da):130,689
Last modified:March 23, 2010 - v3
Checksum:i498231607911400F
GO

Sequence cautioni

The sequence AAD21553 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti171 – 172VA → AR in AAD21553 (Ref. 1) Curated2
Sequence conflicti445V → F in AAD21553 (Ref. 1) Curated1
Sequence conflicti481V → F in AAD21553 (Ref. 1) Curated1
Sequence conflicti1017S → F in AAD21553 (Ref. 1) Curated1
Sequence conflicti1174K → I in AAD21553 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF088896 Genomic DNA. Translation: AAD21553.1. Different initiation.
AE008692 Genomic DNA. Translation: AAV89817.2.
RefSeqiWP_011241016.1. NC_006526.2.

Genome annotation databases

EnsemblBacteriaiAAV89817; AAV89817; ZMO1193.
KEGGizmo:ZMO1193.
PATRICi32567678. VBIZymMob102260_1130.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF088896 Genomic DNA. Translation: AAD21553.1. Different initiation.
AE008692 Genomic DNA. Translation: AAV89817.2.
RefSeqiWP_011241016.1. NC_006526.2.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAV89817; AAV89817; ZMO1193.
KEGGizmo:ZMO1193.
PATRICi32567678. VBIZymMob102260_1130.

Phylogenomic databases

HOGENOMiHOG000004020.
KOiK03168.
OMAiFRSAEYW.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 3 hits.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTOP1_ZYMMO
AccessioniPrimary (citable) accession number: Q9X3X7
Secondary accession number(s): Q5NN93
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: March 23, 2010
Last modified: September 7, 2016
This is version 110 of the entry and version 3 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

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.