DNA topoisomerase 4 subunit A - Escherichia coli (strain K12)

Preferred order of sections

Names and origin

Protein names

Recommended name:
DNA topoisomerase 4 subunit A
EC=5.99.1.3

Alternative name(s):
Topoisomerase IV subunit A

Gene names

Name:	parC
Ordered Locus Names:	b3019, JW2987

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	752 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.5 Ref.8 Ref.9 Ref.10
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. Ref.8 Ref.9 Ref.10
Enzyme regulation	Inhibited by quinolones. Ref.8
Subunit structure	Heterotetramer composed of ParC and ParE. Interacts with MukB. Ref.5 Ref.7 Ref.9 Ref.10
Subcellular location	Cell membrane; Peripheral membrane protein HAMAP-Rule MF_00936.
Sequence similarities	Belongs to the topoisomerase GyrA/ParC subunit family. ParC type 1 subfamily.
Sequence caution	The sequence AAA24297.1 differs from that shown. Reason: Frameshift at position 10.

Ontologies

Keywords
Cellular component	Cell membrane Membrane
Ligand	DNA-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from direct assay Ref.10 Ref.7. Source: EcoliWiki plasmid partitioning Inferred from direct assay PubMed 8104339. Source: EcoliWiki sister chromatid cohesion Inferred from mutant phenotype PubMed 18765793. Source: EcoliWiki
Cellular_component	DNA topoisomerase complex (ATP-hydrolyzing) Inferred from direct assay Ref.7. Source: EcoliWiki chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from direct assay PubMed 1334483. Source: EcoliWiki extrinsic to plasma membrane Inferred from direct assay PubMed 1334483. Source: EcoliWiki nucleoid Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	ATP binding Inferred from electronic annotation. Source: InterPro DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from Biological aspect of Ancestor. Source: RefGenome
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
mukB	P22523	3	EBI-878544,EBI-542943

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 752

752

DNA topoisomerase 4 subunit A HAMAP-Rule MF_00936

PRO_0000145397

Regions

Region

497 – 752

256

Sufficient for MukB binding HAMAP-Rule MF_00936

Sites

Active site

120

1

O-(5'-phospho-DNA)-tyrosine intermediate By similarity

Site

39

1

Interaction with DNA By similarity

Site

75

1

Interaction with DNA By similarity

Site

77

1

Interaction with DNA By similarity

Site

119

1

Transition state stabilizer By similarity

Experimental info

Mutagenesis

80

1

S → L: Confers resistance to quinolones. No effect on catalytic activity. Ref.8

Mutagenesis

84

1

E → K: Strongly reduced enzyme activity. Increases stability of covalent reaction intermediate with DNA. Confers resistance to quinolones. Ref.8

Mutagenesis

84

1

E → P: Confers resistance to quinolones. Ref.8

Secondary structure

1

.

752

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0AFI2 [UniParc].

Last modified December 20, 2005. Version 1.
Checksum: 0D4907E96CEE7086
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FASTA

752

83,831

        10         20         30         40         50         60 
MSDMAERLAL HEFTENAYLN YSMYVIMDRA LPFIGDGLKP VQRRIVYAMS ELGLNASAKF 

        70         80         90        100        110        120 
KKSARTVGDV LGKYHPHGDS ACYEAMVLMA QPFSYRYPLV DGQGNWGAPD DPKSFAAMRY 

       130        140        150        160        170        180 
TESRLSKYSE LLLSELGQGT ADWVPNFDGT LQEPKMLPAR LPNILLNGTT GIAVGMATDI 

       190        200        210        220        230        240 
PPHNLREVAQ AAIALIDQPK TTLDQLLDIV QGPDYPTEAE IITSRAEIRK IYENGRGSVR 

       250        260        270        280        290        300 
MRAVWKKEDG AVVISALPHQ VSGARVLEQI AAQMRNKKLP MVDDLRDESD HENPTRLVIV 

       310        320        330        340        350        360 
PRSNRVDMDQ VMNHLFATTD LEKSYRINLN MIGLDGRPAV KNLLEILSEW LVFRRDTVRR 

       370        380        390        400        410        420 
RLNYRLEKVL KRLHILEGLL VAFLNIDEVI EIIRNEDEPK PALMSRFGLT ETQAEAILEL 

       430        440        450        460        470        480 
KLRHLAKLEE MKIRGEQSEL EKERDQLQGI LASERKMNNL LKKELQADAQ AYGDDRRSPL 

       490        500        510        520        530        540 
QEREEAKAMS EHDMLPSEPV TIVLSQMGWV RSAKGHDIDA PGLNYKAGDS FKAAVKGKSN 

       550        560        570        580        590        600 
QPVVFVDSTG RSYAIDPITL PSARGQGEPL TGKLTLPPGA TVDHMLMESD DQKLLMASDA 

       610        620        630        640        650        660 
GYGFVCTFND LVARNRAGKA LITLPENAHV MPPVVIEDAS DMLLAITQAG RMLMFPVSDL 

       670        680        690        700        710        720 
PQLSKGKGNK IINIPSAEAA RGEDGLAQLY VLPPQSTLTI HVGKRKIKLR PEELQKVTGE 

       730        740        750 
RGRRGTLMRG LQRIDRVEID SPRRASSGDS EE

« Hide

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]. Strain: K12.
[2]	Erratum Kato J., Nishimura Y., Imamura R., Niki H., Hiraga S., Suzuki H. Cell 65:1289-1290(1991)
[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 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: PROTEIN SEQUENCE OF 30-43; 97-113; 201-225 AND 552-564, FUNCTION MODIFIED BY MUKB, INTERACTION WITH MUKB.
[6]	"Characterization of the Escherichia coli gene for 1-acyl-sn-glycerol-3-phosphate acyltransferase (plsC)." Coleman J. Mol. Gen. Genet. 232:295-303(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 724-752.
[7]	"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: SEQUENCE REVISION, SUBUNIT, CHARACTERIZATION. Strain: K12.
[8]	"The Glu-84 of the ParC subunit plays critical roles in both topoisomerase IV-quinolone and topoisomerase IV-DNA interactions." Hiasa H. Biochemistry 41:11779-11785(2002) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF SER-80 AND GLU-84, FUNCTION, ENZYME REGULATION, CATALYTIC ACTIVITY.
[9]	"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, CATALYTIC ACTIVITY.
[10]	"The structural basis for substrate specificity in DNA topoisomerase IV." Corbett K.D., Schoeffler A.J., Thomsen N.D., Berger J.M. J. Mol. Biol. 351:545-561(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 27-752, FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH PARE, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M58408 Genomic DNA. Translation: AAA24297.1. Frameshift.
M63491 Genomic DNA. Translation: AAA24396.1.
U28377 Genomic DNA. Translation: AAA69187.1.
U00096 Genomic DNA. Translation: AAC76055.1.
AP009048 Genomic DNA. Translation: BAE77075.1.
L22025 Unassigned DNA. Translation: AAC36840.1.

PIR

A65089.

RefSeq

NP_417491.1. NC_000913.2.
YP_491211.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZVT	X-ray	1.70	A/B	497-752	[»]
1ZVU	X-ray	3.00	A	27-742	[»]

ProteinModelPortal

P0AFI2.

SMR

P0AFI2. Positions 28-742.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36030N.

IntAct

P0AFI2. 23 interactions.

MINT

MINT-1227290.

STRING

511145.b3019.

Proteomic databases

PaxDb

P0AFI2.

PRIDE

P0AFI2.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76055; AAC76055; b3019.
BAE77075; BAE77075; BAE77075.

GeneID

12933371.
947499.

KEGG

ecj:Y75_p2945.
eco:b3019.

PATRIC

32121452. VBIEscCol129921_3113.

Organism-specific databases

EchoBASE

EB0680.

EcoGene

EG10686. parC.

Phylogenomic databases

eggNOG

COG0188.

HOGENOM

HOG000076277.

KO

K02621.

OMA

YKAGDSY.

ProtClustDB

PRK05561.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10686-MONOMER.
ECOL316407:JW2987-MONOMER.

Gene expression databases

Genevestigator

P0AFI2.

Family and domain databases

Gene3D

3.30.1360.40. 1 hit.
3.90.199.10. 2 hits.

HAMAP

MF_00936. ParC_type1.

InterPro

IPR024946. Arg_repress_C-like.
IPR006691. GyrA/parC_pinwhl.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013760. Topo_IIA_like_dom.
IPR005742. TopoIV_A_Gneg.
[Graphical view]

Pfam

PF03989. DNA_gyraseA_C. 2 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]

SMART

SM00434. TOP4c. 1 hit.
[Graphical view]

SUPFAM

SSF56719. Topo_IIA_cen. 1 hit.

TIGRFAMs

TIGR01062. parC_Gneg. 1 hit.

ProtoNet

Search...

Other

BindingDB

P0AFI2.

ChEMBL

CHEMBL1895.

DrugBank

DB00817. Rosoxacin.

EvolutionaryTrace

P0AFI2.

Entry information

Entry name

PARC_ECOLI

Accession

Primary (citable) accession number: P0AFI2
Secondary accession number(s): O69154, P20082, Q2M9I1

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	December 20, 2005
Last modified:	May 1, 2013
This is version 73 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents