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Protein

DNA topoisomerase 1

Gene

topA

Organism
Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
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 bindingi110 – 1101Magnesium 1; catalyticUniRule annotation
Metal bindingi110 – 1101Magnesium 2UniRule annotation
Metal bindingi112 – 1121Magnesium 2UniRule annotation
Sitei167 – 1671Interaction with DNAUniRule annotation
Sitei168 – 1681Interaction with DNAUniRule annotation
Sitei171 – 1711Interaction with DNAUniRule annotation
Sitei176 – 1761Interaction with DNAUniRule annotation
Sitei183 – 1831Interaction with DNAUniRule annotation
Active sitei318 – 3181O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei320 – 3201Interaction with DNAUniRule annotation
Sitei504 – 5041Interaction with DNAUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri596 – 62833C4-type 1Add
BLAST
Zinc fingeri658 – 68528C4-type 2Add
BLAST
Zinc fingeri707 – 73226C4-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

BioCyciBAPH107806:GBZJ-284-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:BU284
OrganismiBuchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
Taxonomic identifieri107806 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeBuchnera
ProteomesiUP000001806 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 861861DNA topoisomerase 1PRO_0000145144Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi107806.BU284.

Structurei

3D structure databases

ProteinModelPortaliP57371.
SMRiP57371. Positions 2-569, 741-856.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 141139ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni191 – 1966Interaction 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 fingeri596 – 62833C4-type 1Add
BLAST
Zinc fingeri658 – 68528C4-type 2Add
BLAST
Zinc fingeri707 – 73226C4-type 3Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000004018.
KOiK03168.
OMAiVVECDKC.
OrthoDBiEOG6S7XQ9.

Family and domain databases

Gene3Di1.10.460.10. 2 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.
IPR005733. TopoI_bac-type.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[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.

P57371-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQKSLVIVES PAKAKTINQY LGSEYIVKSS IGHIRDLTKG KLYNKEKNKK
60 70 80 90 100
FLNENFIEKT NENKILIKQM GIDPYQNWKF EYHILPGKEK IISELKYIAN
110 120 130 140 150
QVKHIYLATD LDREGEAIAW HLKEVIGGDS SKFSRVVFNE ITQHSIQKAF
160 170 180 190 200
KNVGHINMNR VHAQQARRFM DRIVGYMISP LLWKKIARGL SAGRVQSVAV
210 220 230 240 250
RIIADRESII KNFVPEEYWK LDVSLISQDK KKINMDVTHY NNKKFRPINE
260 270 280 290 300
NEVSFAVEKI QKSSCIVKNY EEKISYLKAP APFITSTLQQ SASLRLGFSV
310 320 330 340 350
KKTMFLAQKL YEEGYITYMR TDSNYLSEYA IKKVRKYIKS NYGSNYLPKE
360 370 380 390 400
PNIYSNEKHS QEAHEAIRPS DIKIKNIDSD HLNSSAKKLY ELIWNQFLAS
410 420 430 440 450
QMKSVKYKSI TVTVLADMFK LQKSERIVMF QGWNKVLIEE KNVFSQFPIL
460 470 480 490 500
QTGSQLFINK VTPSQKFTKP PPRFSEASLV RELEKKGIGR PSTYSAITSK
510 520 530 540 550
IQDRGYVKIK KNKFYAEKMG EILTIRLKKS FSNLIDYNFT AHMEKKLDQV
560 570 580 590 600
AENKVTWRYL LDDFFKKFSE QLEQAKKSPE EGGMELNNIV PTSLNCPICC
610 620 630 640 650
KKMGIKTAIT GVFLSCLGYN NTDNKKRCKK TINLITLNDF NKEQDNQKKI
660 670 680 690 700
SLQLIQKCDI CNMYMDSYFI NEKLKLHICA NNPSCSGYKF EKGVFKSPIY
710 720 730 740 750
LSKTIQCEKC YNNMKLKIGP FGKFFTCINK ICKNTRKILP NGEISDPKLE
760 770 780 790 800
PIPFPELLCK QSDAWFVLRE GISGIFFAAN TFPKSRETRS PFVEELVRFQ
810 820 830 840 850
HLLPEKIYYL SSAPVIDNYG NKTIVCFDKK KKTHYIASKK DGKFTGWSAV
860
FIDQKWCVIN K
Length:861
Mass (Da):99,740
Last modified:December 1, 2000 - v1
Checksum:i903BBF2EA5265599
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000003 Genomic DNA. Translation: BAB12994.1.
RefSeqiNP_240108.1. NC_002528.1.
WP_010896046.1. NC_002528.1.

Genome annotation databases

EnsemblBacteriaiBAB12994; BAB12994; BAB12994.
GeneIDi1109983.
KEGGibuc:BU284.
PATRICi21244092. VBIBucAph127364_0294.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000003 Genomic DNA. Translation: BAB12994.1.
RefSeqiNP_240108.1. NC_002528.1.
WP_010896046.1. NC_002528.1.

3D structure databases

ProteinModelPortaliP57371.
SMRiP57371. Positions 2-569, 741-856.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi107806.BU284.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB12994; BAB12994; BAB12994.
GeneIDi1109983.
KEGGibuc:BU284.
PATRICi21244092. VBIBucAph127364_0294.

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000004018.
KOiK03168.
OMAiVVECDKC.
OrthoDBiEOG6S7XQ9.

Enzyme and pathway databases

BioCyciBAPH107806:GBZJ-284-MONOMER.

Family and domain databases

Gene3Di1.10.460.10. 2 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.
IPR005733. TopoI_bac-type.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[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. "Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS."
    Shigenobu S., Watanabe H., Hattori M., Sakaki Y., Ishikawa H.
    Nature 407:81-86(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: APS.

Entry informationi

Entry nameiTOP1_BUCAI
AccessioniPrimary (citable) accession number: P57371
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: June 24, 2015
This is version 103 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. Buchnera aphidicola (subsp. Acyrthosiphon pisum)
    Buchnera aphidicola (subsp. Acyrthosiphon pisum): entries and gene names
  2. 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.