Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

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



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

Regulation Summary Diagram: ?

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)
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 , Pfam:IN-FAMILY:PF00521 , Pfam:IN-FAMILY:PF03989 , Smart:IN-FAMILY:SM00434

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred by computational analysis Inferred from experiment [Peng93, GOA06, GOA01, GOA01a]
GO:0006265 - DNA topological change Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Peng93, Corbett05]
GO:0007059 - chromosome segregation Inferred from experiment Inferred by computational analysis [GOA06, Corbett05, Kato88]
GO:0007062 - sister chromatid cohesion Inferred from experiment [Wang08a]
GO:0030541 - plasmid partitioning Inferred from experiment [Peng93a]
GO:0006259 - DNA metabolic process Inferred by computational analysis [GOA01a]
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 [UniProtGOA11a, GOA06, GOA01a, Corbett05, Nakajima07]
GO:0005515 - protein binding Inferred from experiment [Vos13, Butland05, Li10b]
GO:0003916 - DNA topoisomerase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0003918 - DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Kato92, Espeli03]
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 [GOA01a]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0009295 - nucleoid Inferred by computational analysis [Gaudet10]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

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

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]
Alternate sequence: S → L; UniProt: Confers resistance to quinolones. No effect on catalytic activity.
Mutagenesis-Variant 84
[Hiasa02, UniProt13]
Alternate sequence: E → P; UniProt: Confers resistance to quinolones.
Alternate sequence: E → K; UniProt: 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
[UniProt10a]
UniProt: O-(5'-phospho-DNA)-tyrosine intermediate; Non-Experimental Qualifier: by similarity;
Protein-Segment 497 -> 752
[UniProt12b]
UniProt: Sufficient for MukB binding; Sequence Annotation Type: region of interest.


Gene Local Context (not to scale): ?

Transcription Unit:

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

Espeli03: 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, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Li10b: 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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12b: 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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords 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

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

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


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 18.5 on Mon Nov 24, 2014, BIOCYC14A.