P20083 (PARE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	630 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Antibiotic resistance
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from Biological aspect of Ancestor. Source: RefGenome DNA-dependent DNA replication Inferred from Biological aspect of Ancestor. Source: RefGenome plasmid partitioning Inferred from direct assay PubMed 8104339. Source: EcoliWiki response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW sister chromatid cohesion Inferred from mutant phenotype PubMed 18765793. Source: EcoliWiki
Cellular_component	chromosome Inferred from electronic annotation. Source: InterPro nucleoid Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from Biological aspect of Ancestor. Source: RefGenome metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 630

630

DNA topoisomerase 4 subunit B HAMAP-Rule MF_00938

PRO_0000145427

Regions

Domain

412 – 525

114

Toprim

Nucleotide binding

110 – 116

7

ATP HAMAP-Rule MF_00938

Sites

Metal binding

418

1

Magnesium 1; catalytic By similarity

Metal binding

490

1

Magnesium 1; catalytic By similarity

Metal binding

490

1

Magnesium 2 By similarity

Metal binding

492

1

Magnesium 2 By similarity

Binding site

5

1

ATP

Binding site

42

1

ATP

Binding site

69

1

ATP

Binding site

334

1

ATP

Site

443

1

Interaction with DNA By similarity

Site

446

1

Interaction with DNA By similarity

Site

497

1

Interaction with DNA By similarity

Site

615

1

Interaction with DNA By similarity

Natural variations

Natural variant

445

1

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

Secondary structure

1

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630

Helix Strand Turn

Details...

Helix

7 – 9

3

Helix

17 – 21

5

Helix

23 – 25

3

Helix

33 – 48

16

Beta strand

53 – 59

7

Beta strand

65 – 69

5

Turn

80 – 82

3

Beta strand

83 – 85

3

Helix

86 – 92

7

Beta strand

96 – 98

3

Beta strand

100 – 104

5

Beta strand

106 – 108

3

Helix

117 – 121

5

Beta strand

123 – 132

10

Beta strand

135 – 142

8

Beta strand

145 – 155

11

Beta strand

162 – 169

8

Helix

171 – 173

3

Helix

181 – 194

14

Beta strand

199 – 204

6

Turn

205 – 208

4

Beta strand

209 – 213

5

Helix

219 – 227

9

Beta strand

233 – 243

11

Beta strand

245 – 255

11

Beta strand

264 – 268

5

Helix

278 – 297

20

Helix

309 – 313

5

Beta strand

316 – 326

11

Beta strand

329 – 331

3

Helix

342 – 359

18

Helix

362 – 382

21

Sequences

	Sequence		Length	Mass (Da)
	P20083 [UniParc]. Last modified February 1, 1994. Version 3. Checksum: 3F83D108BC1C6A41	FASTA	630	70,244
	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

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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.

PIR

D65090.

RefSeq

NP_417502.1. NC_000913.2.
YP_491222.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P20083.

SMR

P20083. Positions 4-383, 388-623.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10441N.

IntAct

P20083. 24 interactions.

MINT

MINT-1223307.

STRING

511145.b3030.

Proteomic databases

PaxDb

P20083.

PRIDE

P20083.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76066; AAC76066; b3030.
BAE77086; BAE77086; BAE77086.

GeneID

12933399.
947501.

KEGG

ecj:Y75_p2956.
eco:b3030.

PATRIC

32121470. VBIEscCol129921_3122.

Organism-specific databases

EchoBASE

EB0681.

EcoGene

EG10687. parE.

Phylogenomic databases

eggNOG

COG0187.

HOGENOM

HOG000075154.

KO

K02622.

OMA

GFIQSYC.

ProtClustDB

PRK05559.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P20083.

Family and domain databases

Gene3D

3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.

HAMAP

MF_00938. ParE_type1.

InterPro

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]

Pfam

PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]

PRINTS

PR00418. TPI2FAMILY.

SMART

SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]

SUPFAM

SSF55874. ATP_bd_ATPase. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.
SSF56719. Topo_IIA_cen. 1 hit.

TIGRFAMs

TIGR01055. parE_Gneg. 1 hit.

PROSITE

PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P20083.

EvolutionaryTrace

P20083.

Entry information

Entry name

PARE_ECOLI

Accession

Primary (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 1, 2013
This is version 121 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program