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Escherichia coli K-12 substr. MG1655 Protein: dimer of topoisomerase IV subunit A



Gene: parC Accession Numbers: EG10686 (EcoCyc), b3019, ECK3010

Regulation Summary Diagram: ?

Regulation summary diagram for parC

Component of: topoisomerase IV (summary available)

Subunit composition of dimer of topoisomerase IV subunit A = [ParC]2
         topoisomerase IV subunit A = ParC

Summary:
The purified ParC protein is a dimer in solution [Peng93].

Locations: inner membrane, bacterial nucleoid, cytosol

Map Position: [3,161,737 <- 3,163,995] (68.15 centisomes, 245°)
Length: 2259 bp / 752 aa

Molecular Weight of Polypeptide: 83.831 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009916 , CGSC:33440 , DIP:DIP-36030N , EchoBASE:EB0680 , EcoGene:EG10686 , EcoliWiki:b3019 , Mint:MINT-1227290 , ModBase:P0AFI2 , OU-Microarray:b3019 , PortEco:parC , PR:PRO_000023493 , Pride:P0AFI2 , Protein Model Portal:P0AFI2 , RefSeq:NP_417491 , RegulonDB:EG10686 , SMR:P0AFI2 , String:511145.b3019 , Swiss-Model:P0AFI2 , UniProt:P0AFI2

Relationship Links: InterPro:IN-FAMILY:IPR002205 , InterPro:IN-FAMILY:IPR005742 , InterPro:IN-FAMILY:IPR006691 , InterPro:IN-FAMILY:IPR013758 , InterPro:IN-FAMILY:IPR013760 , InterPro:IN-FAMILY:IPR024946 , PDB:Structure:1ZVT , PDB:Structure:1ZVU , PDB:Structure:4MN4 , Pfam:IN-FAMILY:PF00521 , Pfam:IN-FAMILY:PF03989 , Smart:IN-FAMILY:SM00434

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006265 - DNA topological change Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Peng93, Corbett05]
GO:0007059 - chromosome segregation Inferred from experiment Inferred by computational analysis [GOA06, Corbett05, Kato88]
GO:0007062 - sister chromatid cohesion Inferred from experiment [Wang08b]
GO:0030541 - plasmid partitioning Inferred from experiment [Peng93a]
GO:0006259 - DNA metabolic process Inferred by computational analysis [GOA01]
GO:0006268 - DNA unwinding involved in DNA replication Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Corbett05, Nakajima07]
GO:0005515 - protein binding Inferred from experiment [Vos13, Butland05, Li10a]
GO:0003916 - DNA topoisomerase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003918 - DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred by computational analysis [GOA06, GOA01a, GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Kato92, Espeli03a]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0009330 - DNA topoisomerase complex (ATP-hydrolyzing) Inferred from experiment [Peng93]
GO:0019897 - extrinsic component of plasma membrane Inferred from experiment Inferred by computational analysis [GOA06, Kato92]
GO:0005694 - chromosome Inferred by computational analysis [GOA01]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0009295 - nucleoid Inferred by computational analysis [Gaudet10]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for parC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

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

Summary:
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 [Kato90]. 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 [Peng93].


Sequence Features

Protein sequence of topoisomerase IV subunit A with features indicated

Feature Class Location Citations Comment
Amino-Acid-Site 39
[UniProt13]
UniProt: Interaction with DNA; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 75
[UniProt13]
UniProt: Interaction with DNA; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Amino-Acid-Site 77
[UniProt13]
UniProt: Interaction with DNA; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 80
[Hiasa02, UniProt13]
UniProt: Confers resistance to quinolones. No effect on catalytic activity.
Mutagenesis-Variant 84
[Hiasa02, UniProt13]
[Hiasa02, UniProt13]
E → P: Confers resistance to quinolones.
E → K: Strongly reduced enzyme activity. Increases stability of covalent reaction intermediate with DNA. Confers resistance to quinolones.
Amino-Acid-Site 119
[UniProt13]
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Active-Site 120
[UniProt10]
UniProt: O-(5'-phospho-DNA)-tyrosine intermediate; Non-Experimental Qualifier: by similarity;
Protein-Segment 497 -> 752
[UniProt12a]
UniProt: Sufficient for MukB binding; Sequence Annotation Type: region of interest.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b3019 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10686; confirmed by SwissProt match.


References

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

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Corbett05: Corbett KD, Schoeffler AJ, Thomsen ND, Berger JM (2005). "The structural basis for substrate specificity in DNA topoisomerase IV." J Mol Biol 351(3);545-61. PMID: 16023670

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

Espeli03a: Espeli O, Levine C, Hassing H, Marians KJ (2003). "Temporal regulation of topoisomerase IV activity in E. coli." Mol Cell 11(1);189-201. PMID: 12535532

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

Hiasa02: Hiasa H (2002). "The Glu-84 of the ParC subunit plays critical roles in both topoisomerase IV-quinolone and topoisomerase IV-DNA interactions." Biochemistry 41(39);11779-85. PMID: 12269820

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

Kato88: Kato J, Nishimura Y, Yamada M, Suzuki H, Hirota Y (1988). "Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli." J Bacteriol 170(9);3967-77. PMID: 2842295

Kato90: 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

Kato92: Kato J, Suzuki H, Ikeda H (1992). "Purification and characterization of DNA topoisomerase IV in Escherichia coli." J Biol Chem 267(36);25676-84. PMID: 1334483

Li10a: Li Y, Stewart NK, Berger AJ, Vos S, Schoeffler AJ, Berger JM, Chait BT, Oakley MG (2010). "Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction." Proc Natl Acad Sci U S A 107(44);18832-7. PMID: 20921377

Nakajima07: Nakajima T, Yasufuku K, Iyoda A, Yoshida S, Suzuki M, Sekine Y, Shibuya K, Hiroshima K, Nakatani Y, Fujisawa T (2007). "The evaluation of lymph node metastasis by endobronchial ultrasound-guided transbronchial needle aspiration: crucial for selection of surgical candidates with metastatic lung tumors." J Thorac Cardiovasc Surg 134(6);1485-90. PMID: 18023670

Peng93: 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

Peng93a: 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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

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

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Vos13: Vos SM, Stewart NK, Oakley MG, Berger JM (2013). "Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo." EMBO J. PMID: 24097060

Wang08b: 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

Yamamoto09: Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H (2009). "Update on the Keio collection of Escherichia coli single-gene deletion mutants." Mol Syst Biol 5;335. PMID: 20029369


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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