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P20083 (PARE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 131. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA topoisomerase 4 subunit B

EC=5.99.1.3
Alternative name(s):
Topoisomerase IV subunit B
Gene names
Name:parE
Synonyms:nfxD
Ordered Locus Names:b3030, JW2998
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length630 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6 Ref.7 Ref.9

Catalytic activity

ATP-dependent breakage, passage and rejoining of double-stranded DNA. Ref.6 Ref.7

Cofactor

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+. Ref.6

Subunit structure

Heterotetramer composed of ParC and ParE. Ref.6 Ref.7

Sequence similarities

Belongs to the type II topoisomerase family. ParE type 1 subfamily.

Contains 1 Toprim domain.

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 630630DNA topoisomerase 4 subunit B HAMAP-Rule MF_00938
PRO_0000145427

Regions

Domain412 – 525114Toprim
Nucleotide binding110 – 1167ATP HAMAP-Rule MF_00938

Sites

Metal binding4181Magnesium 1; catalytic By similarity
Metal binding4901Magnesium 1; catalytic By similarity
Metal binding4901Magnesium 2 By similarity
Metal binding4921Magnesium 2 By similarity
Binding site51ATP
Binding site421ATP
Binding site691ATP
Binding site3341ATP
Site4431Interaction with DNA By similarity
Site4461Interaction with DNA By similarity
Site4971Interaction with DNA By similarity
Site6151Interaction with DNA By similarity

Natural variations

Natural variant4451L → H in strain: DH161; quinolone-resistant. Ref.8

Secondary structure

............................................................. 630
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P20083 [UniParc].

Last modified February 1, 1994. Version 3.
Checksum: 3F83D108BC1C6A41

FASTA63070,244
        10         20         30         40         50         60 
MTQTYNADAI EVLTGLEPVR RRPGMYTDTT RPNHLGQEVI DNSVDEALAG HAKRVDVILH 

        70         80         90        100        110        120 
ADQSLEVIDD GRGMPVDIHP EEGVPAVELI LCRLHAGGKF SNKNYQFSGG LHGVGISVVN 

       130        140        150        160        170        180 
ALSKRVEVNV RRDGQVYNIA FENGEKVQDL QVVGTCGKRN TGTSVHFWPD ETFFDSPRFS 

       190        200        210        220        230        240 
VSRLTHVLKA KAVLCPGVEI TFKDEINNTE QRWCYQDGLN DYLAEAVNGL PTLPEKPFIG 

       250        260        270        280        290        300 
NFAGDTEAVD WALLWLPEGG ELLTESYVNL IPTMQGGTHV NGLRQGLLDA MREFCEYRNI 

       310        320        330        340        350        360 
LPRGVKLSAE DIWDRCAYVL SVKMQDPQFA GQTKERLSSR QCAAFVSGVV KDAFILWLNQ 

       370        380        390        400        410        420 
NVQAAELLAE MAISSAQRRM RAAKKVVRKK LTSGPALPGK LADCTAQDLN RTELFLVEGD 

       430        440        450        460        470        480 
SAGGSAKQAR DREYQAIMPL KGKILNTWEV SSDEVLASQE VHDISVAIGI DPDSDDLSQL 

       490        500        510        520        530        540 
RYGKICILAD ADSDGLHIAT LLCALFVKHF RALVKHGHVY VALPPLYRID LGKEVYYALT 

       550        560        570        580        590        600 
EEEKEGVLEQ LKRKKGKPNV QRFKGLGEMN PMQLRETTLD PNTRRLVQLT IDDEDDQRTD 

       610        620        630 
AMMDMLLAKK RSEDRRNWLQ EKGDMAEIEV 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRD65090.
RefSeqNP_417502.1. NC_000913.3.
YP_491222.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1S14X-ray2.00A/B1-217[»]
1S16X-ray2.10A/B1-390[»]
3FV5X-ray1.80A/B15-215[»]
4HZ0X-ray2.20A/B12-216[»]
ProteinModelPortalP20083.
SMRP20083. Positions 4-383, 388-623.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10441N.
IntActP20083. 24 interactions.
MINTMINT-1223307.
STRING511145.b3030.

Chemistry

BindingDBP20083.
ChEMBLCHEMBL2363076.

Proteomic databases

PaxDbP20083.
PRIDEP20083.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76066; AAC76066; b3030.
BAE77086; BAE77086; BAE77086.
GeneID12933399.
947501.
KEGGecj:Y75_p2956.
eco:b3030.
PATRIC32121470. VBIEscCol129921_3122.

Organism-specific databases

EchoBASEEB0681.
EcoGeneEG10687. parE.

Phylogenomic databases

eggNOGCOG0187.
HOGENOMHOG000075154.
KOK02622.
OMAQSYNADA.
OrthoDBEOG6P334W.
PhylomeDBP20083.

Enzyme and pathway databases

BioCycEcoCyc:EG10687-MONOMER.
ECOL316407:JW2998-MONOMER.

Gene expression databases

GenevestigatorP20083.

Family and domain databases

Gene3D3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPMF_00938. ParE_type1.
InterProIPR002288. 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]
PfamPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSPR00418. TPI2FAMILY.
SMARTSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsTIGR01055. parE_Gneg. 1 hit.
PROSITEPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP20083.
PROP20083.

Entry information

Entry namePARE_ECOLI
AccessionPrimary (citable) accession number: P20083
Secondary accession number(s): Q2M9H0
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1994
Last modified: May 14, 2014
This is version 131 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene