Escherichia coli K-12 substr. MG1655 Polypeptide: topoisomerase IV subunit B

Gene: parE Accession Numbers: EG10687 (EcoCyc), b3030, ECK3021

Synonyms: nfxD

Regulation Summary Diagram: ?

Regulation summary diagram for parE

Component of: topoisomerase IV (summary available)

The crystal structures of two N-terminal fragments of ParE have been solved [Bellon04].

Locations: bacterial nucleoid, cytosol

Map Position: [3,171,526 <- 3,173,418] (68.36 centisomes, 246°)
Length: 1893 bp / 630 aa

Molecular Weight of Polypeptide: 70.244 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009950 , CGSC:33451 , DIP:DIP-10441N , EchoBASE:EB0681 , EcoGene:EG10687 , EcoliWiki:b3030 , Mint:MINT-1223307 , ModBase:P20083 , OU-Microarray:b3030 , PortEco:parE , PR:PRO_000023494 , Pride:P20083 , Protein Model Portal:P20083 , RefSeq:NP_417502 , RegulonDB:EG10687 , SMR:P20083 , String:511145.b3030 , UniProt:P20083

Relationship Links: InterPro:IN-FAMILY:IPR001241 , InterPro:IN-FAMILY:IPR002288 , InterPro:IN-FAMILY:IPR003594 , InterPro:IN-FAMILY:IPR005737 , InterPro:IN-FAMILY:IPR006171 , InterPro:IN-FAMILY:IPR013506 , InterPro:IN-FAMILY:IPR013759 , InterPro:IN-FAMILY:IPR013760 , InterPro:IN-FAMILY:IPR014721 , InterPro:IN-FAMILY:IPR018522 , InterPro:IN-FAMILY:IPR020568 , PDB:Structure:1S14 , PDB:Structure:1S16 , PDB:Structure:3FV5 , PDB:Structure:4HZ0 , Pfam:IN-FAMILY:PF00204 , Pfam:IN-FAMILY:PF00986 , Pfam:IN-FAMILY:PF01751 , Pfam:IN-FAMILY:PF02518 , Prints:IN-FAMILY:PR00418 , Prosite:IN-FAMILY:PS00177 , Prosite:IN-FAMILY:PS50880 , Smart:IN-FAMILY:SM00387 , Smart:IN-FAMILY:SM00433

In Paralogous Gene Group: 480 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for parE

GO Terms:

Biological Process: GO:0007062 - sister chromatid cohesion Inferred from experiment [Wang08a]
GO:0030541 - plasmid partitioning Inferred from experiment [Peng93]
GO:0051276 - chromosome organization Inferred from experiment [Wang08a]
GO:0006265 - DNA topological change Inferred by computational analysis [GOA06, GOA01, Gaudet10]
GO:0006268 - DNA unwinding involved in DNA replication Inferred by computational analysis [Gaudet10]
GO:0007059 - chromosome segregation Inferred by computational analysis [Gaudet10, GOA06]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0003916 - DNA topoisomerase activity Inferred by computational analysis [UniProtGOA11]
GO:0003918 - DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred by computational analysis [GOA06, GOA01a, GOA01, Gaudet10]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005694 - chromosome Inferred by computational analysis [GOA01]
GO:0009295 - nucleoid Inferred by computational analysis [Gaudet10]
GO:0009330 - DNA topoisomerase complex (ATP-hydrolyzing) Inferred by computational analysis [Gaudet10]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for parE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Subunit of: topoisomerase IV

Subunit composition of topoisomerase IV = [ParE]2[(ParC)2]
         topoisomerase IV subunit B = ParE (summary available)
         dimer of topoisomerase IV subunit A = (ParC)2
                 topoisomerase IV subunit A = ParC

Topoisomerase IV belongs to the type II topoisomerase family; it can remove double-stranded DNA crossings [Ullsperger96] and is essential for progression of the replication fork [Grompone04] and chromosome segregation after replication [Kato90a]. Topoisomerase IV decatenates the two daughter molecules after DNA replication and is able to relax both positive and negative DNA supercoils. Positive supercoils are relaxed at a 20-fold faster rate than negative supercoils [Crisona00]. The enzyme is ATP-dependent.

The minimum duplex length for topoisomerase IV function is 40 bp [Belotserkovskii06].

Active Topoisomerase IV is a complex of two subunits each of the ParC and ParE polypeptides [Peng93a].

Sequence Features

Protein sequence of topoisomerase IV subunit B with features indicated

Feature Class Location Attached Group Citations Comment
Amino-Acid-Sites-That-Bind 5  
UniProt: ATP.
Amino-Acid-Sites-That-Bind 42  
UniProt: ATP.
Amino-Acid-Sites-That-Bind 69  
UniProt: ATP.
Nucleotide-Phosphate-Binding-Region 110 -> 116 ATP
UniProt: ATP.
Amino-Acid-Sites-That-Bind 334  
UniProt: ATP.
Conserved-Region 412 -> 525  
UniProt: Toprim.
Metal-Binding-Site 418  
UniProt: Magnesium 1; catalytic; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 443  
UniProt: Interaction with DNA; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Extrinsic-Sequence-Variant 445  
[Breines97, UniProt11]
UniProt: (in strain: DH161; quinolone- resistant).
Amino-Acid-Site 446  
UniProt: Interaction with DNA; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 490  
UniProt: Magnesium 1; catalytic; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 492  
UniProt: Magnesium 2; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 497  
UniProt: Interaction with DNA; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 615  
UniProt: Interaction with DNA; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3030 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10687; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bellon04: Bellon S, Parsons JD, Wei Y, Hayakawa K, Swenson LL, Charifson PS, Lippke JA, Aldape R, Gross CH (2004). "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." Antimicrob Agents Chemother 48(5);1856-64. PMID: 15105144

Belotserkovskii06: Belotserkovskii BP, Arimondo PB, Cozzarelli NR (2006). "Topoisomerase action on short DNA duplexes reveals requirements for gate and transfer DNA segments." J Biol Chem 281(35);25407-15. PMID: 16798730

Breines97: Breines DM, Ouabdesselam S, Ng EY, Tankovic J, Shah S, Soussy CJ, Hooper DC (1997). "Quinolone resistance locus nfxD of Escherichia coli is a mutant allele of the parE gene encoding a subunit of topoisomerase IV." Antimicrob Agents Chemother 41(1);175-9. PMID: 8980775

Crisona00: Crisona NJ, Strick TR, Bensimon D, Croquette V, Cozzarelli NR (2000). "Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements." Genes Dev 14(22);2881-92. PMID: 11090135

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Grompone04: Grompone G, Bidnenko V, Ehrlich SD, Michel B (2004). "PriA is essential for viability of the Escherichia coli topoisomerase IV parE10(Ts) mutant." J Bacteriol 186(4);1197-9. PMID: 14762016

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kato90a: Kato J, Nishimura Y, Imamura R, Niki H, Hiraga S, Suzuki H (1990). "New topoisomerase essential for chromosome segregation in E. coli." Cell 63(2);393-404. PMID: 2170028

Peng93: Peng H, Marians KJ (1993). "Decatenation activity of topoisomerase IV during oriC and pBR322 DNA replication in vitro." Proc Natl Acad Sci U S A 90(18);8571-5. PMID: 8104339

Peng93a: Peng H, Marians KJ (1993). "Escherichia coli topoisomerase IV. Purification, characterization, subunit structure, and subunit interactions." J Biol Chem 268(32);24481-90. PMID: 8227000

Ullsperger96: Ullsperger C, Cozzarelli NR (1996). "Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Escherichia coli." J Biol Chem 271(49);31549-55. PMID: 8940171

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wang08a: Wang X, Reyes-Lamothe R, Sherratt DJ (2008). "Modulation of Escherichia coli sister chromosome cohesion by topoisomerase IV." Genes Dev 22(17);2426-33. PMID: 18765793

Other References Related to Gene Regulation

Avison01: Avison MB, Horton RE, Walsh TR, Bennett PM (2001). "Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media." J Biol Chem 276(29);26955-61. PMID: 11350954

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Oct 6, 2015, biocyc13.