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P20083

- PARE_ECOLI

UniProt

P20083 - PARE_ECOLI

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Protein
DNA topoisomerase 4 subunit B
Gene
parE, nfxD, b3030, JW2998
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule. MukB stimulates the relaxation activity of topoisomerase IV and also has a modest effect on decatenation.3 Publications

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.2 Publications

Cofactori

Magnesium. Binds two Mg2+ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ and Ca2+.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei5 – 51ATP
Binding sitei42 – 421ATP
Binding sitei69 – 691ATP
Binding sitei334 – 3341ATP
Metal bindingi418 – 4181Magnesium 1; catalytic By similarity
Sitei443 – 4431Interaction with DNA By similarity
Sitei446 – 4461Interaction with DNA By similarity
Metal bindingi490 – 4901Magnesium 1; catalytic By similarity
Metal bindingi490 – 4901Magnesium 2 By similarity
Metal bindingi492 – 4921Magnesium 2 By similarity
Sitei497 – 4971Interaction with DNA By similarity
Sitei615 – 6151Interaction with DNA By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi110 – 1167ATPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: RefGenome
  4. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. DNA topological change Source: RefGenome
  3. DNA unwinding involved in DNA replication Source: RefGenome
  4. chromosome organization Source: EcoliWiki
  5. plasmid partitioning Source: EcoliWiki
  6. response to antibiotic Source: UniProtKB-KW
  7. sister chromatid cohesion Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Antibiotic resistance

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10687-MONOMER.
ECOL316407:JW2998-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 4 subunit B (EC:5.99.1.3)
Alternative name(s):
Topoisomerase IV subunit B
Gene namesi
Name:parE
Synonyms:nfxD
Ordered Locus Names:b3030, JW2998
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10687. parE.

Subcellular locationi

GO - Cellular componenti

  1. DNA topoisomerase complex (ATP-hydrolyzing) Source: RefGenome
  2. chromosome Source: InterPro
  3. nucleoid Source: RefGenome
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 630630DNA topoisomerase 4 subunit BUniRule annotation
PRO_0000145427Add
BLAST

Proteomic databases

PaxDbiP20083.
PRIDEiP20083.

Expressioni

Gene expression databases

GenevestigatoriP20083.

Interactioni

Subunit structurei

Heterotetramer composed of ParC and ParE.2 Publications

Protein-protein interaction databases

DIPiDIP-10441N.
IntActiP20083. 24 interactions.
MINTiMINT-1223307.
STRINGi511145.b3030.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 93
Helixi17 – 215
Helixi23 – 253
Helixi33 – 4816
Beta strandi53 – 597
Beta strandi65 – 695
Turni80 – 823
Beta strandi83 – 853
Helixi86 – 927
Beta strandi96 – 983
Beta strandi100 – 1045
Beta strandi106 – 1083
Helixi117 – 1215
Beta strandi123 – 13210
Beta strandi135 – 1428
Beta strandi145 – 15511
Beta strandi162 – 1698
Helixi171 – 1733
Helixi181 – 19414
Beta strandi199 – 2046
Turni205 – 2084
Beta strandi209 – 2135
Helixi219 – 2279
Beta strandi233 – 24311
Beta strandi245 – 25511
Beta strandi264 – 2685
Helixi278 – 29720
Helixi309 – 3135
Beta strandi316 – 32611
Beta strandi329 – 3313
Helixi342 – 35918
Helixi362 – 38221

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S14X-ray2.00A/B1-217[»]
1S16X-ray2.10A/B1-390[»]
3FV5X-ray1.80A/B15-215[»]
4HZ0X-ray2.20A/B12-216[»]
ProteinModelPortaliP20083.
SMRiP20083. Positions 4-383, 388-623.

Miscellaneous databases

EvolutionaryTraceiP20083.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini412 – 525114Toprim
Add
BLAST

Sequence similaritiesi

Contains 1 Toprim domain.

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075154.
KOiK02622.
OMAiQSYNADA.
OrthoDBiEOG6P334W.
PhylomeDBiP20083.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_00938. ParE_type1.
InterProiIPR002288. DNA_gyrase_B_C.
IPR003594. HATPase_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR005737. TopoIV_B_Gneg.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01055. parE_Gneg. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P20083-1 [UniParc]FASTAAdd to Basket

« Hide

MTQTYNADAI EVLTGLEPVR RRPGMYTDTT RPNHLGQEVI DNSVDEALAG    50
HAKRVDVILH ADQSLEVIDD GRGMPVDIHP EEGVPAVELI LCRLHAGGKF 100
SNKNYQFSGG LHGVGISVVN ALSKRVEVNV RRDGQVYNIA FENGEKVQDL 150
QVVGTCGKRN TGTSVHFWPD ETFFDSPRFS VSRLTHVLKA KAVLCPGVEI 200
TFKDEINNTE QRWCYQDGLN DYLAEAVNGL PTLPEKPFIG NFAGDTEAVD 250
WALLWLPEGG ELLTESYVNL IPTMQGGTHV NGLRQGLLDA MREFCEYRNI 300
LPRGVKLSAE DIWDRCAYVL SVKMQDPQFA GQTKERLSSR QCAAFVSGVV 350
KDAFILWLNQ NVQAAELLAE MAISSAQRRM RAAKKVVRKK LTSGPALPGK 400
LADCTAQDLN RTELFLVEGD SAGGSAKQAR DREYQAIMPL KGKILNTWEV 450
SSDEVLASQE VHDISVAIGI DPDSDDLSQL RYGKICILAD ADSDGLHIAT 500
LLCALFVKHF RALVKHGHVY VALPPLYRID LGKEVYYALT EEEKEGVLEQ 550
LKRKKGKPNV QRFKGLGEMN PMQLRETTLD PNTRRLVQLT IDDEDDQRTD 600
AMMDMLLAKK RSEDRRNWLQ EKGDMAEIEV 630
Length:630
Mass (Da):70,244
Last modified:February 1, 1994 - v3
Checksum:i3F83D108BC1C6A41
GO

Sequence cautioni

The sequence AAA24298.1 differs from that shown. Reason: Frameshift at position 597.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti445 – 4451L → H in strain: DH161; quinolone-resistant. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M58409 Genomic DNA. Translation: AAA24298.1. Frameshift.
U28377 Genomic DNA. Translation: AAA69198.1.
U00096 Genomic DNA. Translation: AAC76066.1.
AP009048 Genomic DNA. Translation: BAE77086.1.
L22026 Unassigned DNA. Translation: AAC36841.1.
PIRiD65090.
RefSeqiNP_417502.1. NC_000913.3.
YP_491222.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76066; AAC76066; b3030.
BAE77086; BAE77086; BAE77086.
GeneIDi12933399.
947501.
KEGGiecj:Y75_p2956.
eco:b3030.
PATRICi32121470. VBIEscCol129921_3122.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M58409 Genomic DNA. Translation: AAA24298.1 . Frameshift.
U28377 Genomic DNA. Translation: AAA69198.1 .
U00096 Genomic DNA. Translation: AAC76066.1 .
AP009048 Genomic DNA. Translation: BAE77086.1 .
L22026 Unassigned DNA. Translation: AAC36841.1 .
PIRi D65090.
RefSeqi NP_417502.1. NC_000913.3.
YP_491222.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1S14 X-ray 2.00 A/B 1-217 [» ]
1S16 X-ray 2.10 A/B 1-390 [» ]
3FV5 X-ray 1.80 A/B 15-215 [» ]
4HZ0 X-ray 2.20 A/B 12-216 [» ]
ProteinModelPortali P20083.
SMRi P20083. Positions 4-383, 388-623.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-10441N.
IntActi P20083. 24 interactions.
MINTi MINT-1223307.
STRINGi 511145.b3030.

Chemistry

BindingDBi P20083.
ChEMBLi CHEMBL2363076.

Proteomic databases

PaxDbi P20083.
PRIDEi P20083.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76066 ; AAC76066 ; b3030 .
BAE77086 ; BAE77086 ; BAE77086 .
GeneIDi 12933399.
947501.
KEGGi ecj:Y75_p2956.
eco:b3030.
PATRICi 32121470. VBIEscCol129921_3122.

Organism-specific databases

EchoBASEi EB0681.
EcoGenei EG10687. parE.

Phylogenomic databases

eggNOGi COG0187.
HOGENOMi HOG000075154.
KOi K02622.
OMAi QSYNADA.
OrthoDBi EOG6P334W.
PhylomeDBi P20083.

Enzyme and pathway databases

BioCyci EcoCyc:EG10687-MONOMER.
ECOL316407:JW2998-MONOMER.

Miscellaneous databases

EvolutionaryTracei P20083.
PROi P20083.

Gene expression databases

Genevestigatori P20083.

Family and domain databases

Gene3Di 3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPi MF_00938. ParE_type1.
InterProi IPR002288. DNA_gyrase_B_C.
IPR003594. HATPase_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR005737. TopoIV_B_Gneg.
IPR006171. Toprim_domain.
[Graphical view ]
Pfami PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00418. TPI2FAMILY.
SMARTi SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsi TIGR01055. parE_Gneg. 1 hit.
PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "New topoisomerase essential for chromosome segregation in E. coli."
    Kato J., Nishimura Y., Imamura R., Niki H., Hiraga S., Suzuki H.
    Cell 63:393-404(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-602.
    Strain: K12.
  2. "Molecular characterization of the Salmonella typhimurium parE gene."
    Springer A.L., Schmid M.B.
    Nucleic Acids Res. 21:1805-1809(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION TO C-TERMINUS.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Escherichia coli topoisomerase IV. Purification, characterization, subunit structure, and subunit interactions."
    Peng H., Marians K.J.
    J. Biol. Chem. 268:24481-24490(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 588-630, CHARACTERIZATION.
    Strain: K12.
  6. "Use of divalent metal ions in the DNA cleavage reaction of topoisomerase IV."
    Pitts S.L., Liou G.F., Mitchenall L.A., Burgin A.B., Maxwell A., Neuman K.C., Osheroff N.
    Nucleic Acids Res. 39:4808-4817(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, COFACTOR, PUTATIVE METAL-BINDING SITES, CATALYTIC ACTIVITY.
  7. "Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase."
    Bellon S., Parsons J.D., Wei Y., Hayakawa K., Swenson L.L., Charifson P.S., Lippke J.A., Aldape R., Gross C.H.
    Antimicrob. Agents Chemother. 48:1856-1864(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-390 IN COMPLEXES WITH NOVOBIOCIN AND ADENYLYL-IMIDODIPHOSPHATE, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT.
  8. "Quinolone resistance locus nfxD of Escherichia coli is a mutant allele of the parE gene encoding a subunit of topoisomerase IV."
    Breines D.M., Ouabdesselam S., Ng E.Y., Tankovic J., Shah S., Soussy C.J., Hooper D.C.
    Antimicrob. Agents Chemother. 41:175-179(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT QUINOLONE-RESISTANT HIS-445.
  9. "Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction."
    Li Y., Stewart N.K., Berger A.J., Vos S., Schoeffler A.J., Berger J.M., Chait B.T., Oakley M.G.
    Proc. Natl. Acad. Sci. U.S.A. 107:18832-18837(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION MODIFIED BY MUKB.

Entry informationi

Entry nameiPARE_ECOLI
AccessioniPrimary (citable) accession number: P20083
Secondary accession number(s): Q2M9H0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1994
Last modified: September 3, 2014
This is version 132 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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