|Gene:||gyrB||Accession Numbers: EG10424 (EcoCyc), b3699, ECK3691|
Synonyms: cou, hopA, pcpA, pcbA, parA, nalC, Cou, acrB, himB, hisU
Component of: DNA gyrase (extended summary available)
The GyrB subunit of DNA gyrase is required for the ATPase activity of the enzyme. Novobiocin and other coumarin antibiotics are competitive inhibitors of the ATPase activity [Staudenbauer81].
GyrB contains a sizeable insert sequence in its TOPRIM domain that is present in many gram-negative bacteria but not common in other organisms. A crystal structure to 3.1 Å resolution of a GyrBA fusion suggests that this insert "braces" the TOPRIM domain in GyrB against its binding surface in GyrA. Deletion analysis shows that this region is critical for positive and negative supercoiling, and although it does not bind DNA, is required for DNA binding by GyrB [Schoeffler10].
A gyrBpriA double null is inviable [Grompone03].
Gene Citations: [Adachi84]
Locations: bacterial nucleoid, cytosol
|Map Position: [3,875,728 <- 3,878,142] (83.53 centisomes, 301°)||Length: 2415 bp / 804 aa|
Molecular Weight of Polypeptide: 89.95 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0012093 , CGSC:650 , DIP:DIP-48005N , EchoBASE:EB0419 , EcoGene:EG10424 , EcoliWiki:b3699 , OU-Microarray:b3699 , PortEco:gyrB , PR:PRO_000022856 , Pride:P0AES6 , Protein Model Portal:P0AES6 , RefSeq:YP_026241 , RegulonDB:EG10424 , SMR:P0AES6 , String:511145.b3699 , Swiss-Model:P0AES6 , UniProt:P0AES6
Relationship Links: InterPro:IN-FAMILY:IPR001241 , InterPro:IN-FAMILY:IPR002288 , InterPro:IN-FAMILY:IPR003594 , InterPro:IN-FAMILY:IPR006171 , InterPro:IN-FAMILY:IPR011557 , 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:1AJ6 , PDB:Structure:1EI1 , PDB:Structure:1KZN , PDB:Structure:3G7E , PDB:Structure:3NUH , PDB:Structure:4DUH , PDB:Structure:4HYP , PDB:Structure:4KFG , PDB:Structure:4PRV , PDB:Structure:4PRX , PDB:Structure:4PU9 , 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)
|Biological Process:||GO:0006265 - DNA topological change
GO:0006351 - transcription, DNA-templated [Peter04]
GO:0042493 - response to drug [Tsai97]
GO:0006261 - DNA-dependent DNA replication [GOA06]
GO:0006268 - DNA unwinding involved in DNA replication [Gaudet10]
GO:0007059 - chromosome segregation [Gaudet10]
GO:0046677 - response to antibiotic [UniProtGOA11a]
|Molecular Function:||GO:0003677 - DNA binding
[UniProtGOA11a, GOA06, GOA01a, Higgins82, Chatterji00]
GO:0003918 - DNA topoisomerase type II (ATP-hydrolyzing) activity [GOA06, GOA01, GOA01a, Sugino78]
GO:0005515 - protein binding [Butland05]
GO:0005524 - ATP binding [UniProtGOA11a, GOA06, GOA01a, Kampranis98]
GO:0008094 - DNA-dependent ATPase activity [Maxwell84]
GO:0000166 - nucleotide binding [UniProtGOA11a]
GO:0000287 - magnesium ion binding [GOA06]
GO:0003916 - DNA topoisomerase activity [UniProtGOA11a]
GO:0016853 - isomerase activity [UniProtGOA11a]
GO:0046872 - metal ion binding [UniProtGOA11a]
|Cellular Component:||GO:0005737 - cytoplasm
[UniProtGOA11, UniProtGOA11a, GOA06, Thornton94]
GO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0009330 - DNA topoisomerase complex (ATP-hydrolyzing) [Higgins78a]
GO:0005694 - chromosome [GOA01a]
GO:0009295 - nucleoid [Gaudet10]
|MultiFun Terms:||information transfer → DNA related → DNA replication|
|information transfer → RNA related → Transcription related|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Subunit of: DNA gyrase
Synonyms: Topoisomerase II
DNA gyrase is one of two essential members of the type II topoisomerase family in E. coli. It carries out ATP-dependent supercoiling of chromosomal DNA, as well as potentially being involved in decatenation of newly synthesized chrosomal and plasmid DNA.
Gyrase consists of 2 GyrA and 2 GyrB subunits [Sugino80]. The GyrA amino-termini form a dimeric core flanked by their carboxy-terminal domains, which form spirals that wrap the target DNA [Costenaro05, Ruthenburg05]. These GyrA carboxy-terminal domains impart unidirectionality on gyrase supercoiling activity [Ruthenburg05]. The GyrB amino-terminal domain contains the gyrase ATPase activity and is the binding site for antibiotics that inhibit gyrase function [Ali93, Lewis96]. GyrB dimerizes in a "V" shape, with the amino-termini coming together at the base to form the 20 Å ATP-operated DNA-binding clamp and the carboxy-termini at the ends of the "V" involved in protein-protein interaction [Wigley91, Celia94, Brino00, Williams01]. Other studies of the full gyrase tetramer have been carried out in the presence and absence of bound substrate [Krueger90, Sissi05, Blandamer94, Morais97].
Gyrase supercoils and relaxes DNA by cleaving one duplex strand entirely and passing the other, intact DNA duplex through it. The initial gyrase cleavage leaves a staggered cut with 5' overhangs, which romain covalently attached to the GyrA subunits throughout strand transfer [Morrison79]. Indeed, inhibiting the gyrase ATPase stalls the reaction in the middle, yielding double-strand breaks with GyrA monomers attached to each 5' overhang [Sugino80, Gellert79]. DNA supercoiling appears to operate through a two-gate mechanism in which the non-cleaved DNA strand is loaded into the amino-terminal, ATP-dependent clamp formed by dimerized GyrB and then passed through the gap in the bound, cleaved strand [Williams99a, Kampranis99]. When this clamp domain is experimentally locked in the closed conformation, gyrase is no longer able to supercoil DNA, but can still carry out a single relaxation reaction [Williams01]. Each round of supercoiling represents a calculated free energy change of 2.6 kJ/mol and requires ATP [Cullis92, Sugino80a]. The mechanics of gyrase function, including its response to tension in DNA, have been examined at the molecular level [Gore06].
In addition to supercoiling and relaxing DNA, gyrase can also separate catenated DNA, straighten knotted DNA and act in deletion of a region flanked by direct repeats [Marians87, Mizuuchi80, MiuraMasuda90].
Gyrase binds a 120-bp area, with DNA apparently wrapped around the enzyme [Fisher81]. The minimum duplex length for gyrase action is about half that, at 50-60 bp, although it is much less efficient at this length [Belotserkovskii06]. Although there are no canonical cleavage sequences for gyrase, a TG doublet is present at most cut sites [Morrison79]. In addition, gyrase binds to repetitive extragenic palindromic (REP) sequences 10 times more effectively than to random DNA [Yang88].
Gyrase activity is halted by the toxic plasmid-encoded protein CcdB, which interacts with GyrA to wedge gyrase open, locking it in its ATP-bound form [Kampranis99a, DaoThi05, Smith06]. A crystal structure of CcdB has been determined [Loris99].
|Cellular Component:||GO:0005829 - cytosol|
Enzymatic reaction of: gyrase
EC Number: 18.104.22.168
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.
Reversibility of this reaction is unspecified.
|Chain||2 -> 804|
|Conserved-Region||418 -> 533|
|Metal-Binding-Site||424, 498, 500, 502|
|Extrinsic-Sequence-Variant||759 -> 760|
10/20/97 Gene b3699 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10424; confirmed by SwissProt match.
Ali93: Ali JA, Jackson AP, Howells AJ, Maxwell A (1993). "The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs." Biochemistry 32(10);2717-24. PMID: 8383523
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
Blandamer94: Blandamer MJ, Briggs B, Cullis PM, Jackson AP, Maxwell A, Reece RJ (1994). "Domain structure of Escherichia coli DNA gyrase as revealed by differential scanning calorimetry." Biochemistry 33(24);7510-6. PMID: 8011616
Brino00: Brino L, Urzhumtsev A, Mousli M, Bronner C, Mitschler A, Oudet P, Moras D (2000). "Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center." J Biol Chem 275(13);9468-75. PMID: 10734094
Burland93: Burland V, Plunkett G, Daniels DL, Blattner FR (1993). "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Genomics 1993;16(3);551-61. PMID: 7686882
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
Celia94: Celia H, Hoermann L, Schultz P, Lebeau L, Mallouh V, Wigley DB, Wang JC, Mioskowski C, Oudet P (1994). "Three-dimensional model of Escherichia coli gyrase B subunit crystallized in two-dimensions on novobiocin-linked phospholipid films." J Mol Biol 236(2);618-28. PMID: 8107146
Chatterji00: Chatterji M, Unniraman S, Maxwell A, Nagaraja V (2000). "The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding." J Biol Chem 275(30);22888-94. PMID: 10764756
Costenaro05: Costenaro L, Grossmann JG, Ebel C, Maxwell A (2005). "Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit." Structure 13(2);287-96. PMID: 15698572
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
Fairweather80: Fairweather NF, Orr E, Holland IB (1980). "Inhibition of deoxyribonucleic acid gyrase: effects on nucleic acid synthesis and cell division in Escherichia coli K-12." J Bacteriol 142(1);153-61. PMID: 6154685
Funatsuki97: Funatsuki K, Tanaka R, Inagaki S, Konno H, Katoh K, Nakamura H (1997). "acrB mutation located at carboxyl-terminal region of gyrase B subunit reduces DNA binding of DNA gyrase." J Biol Chem 272(20);13302-8. PMID: 9148951
Higgins78a: Higgins NP, Peebles CL, Sugino A, Cozzarelli NR (1978). "Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity." Proc Natl Acad Sci U S A 75(4);1773-7. PMID: 347446
Kampranis99a: Kampranis SC, Howells AJ, Maxwell A (1999). "The interaction of DNA gyrase with the bacterial toxin CcdB: evidence for the existence of two gyrase-CcdB complexes." J Mol Biol 293(3);733-44. PMID: 10543963
Khodursky00: Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR (2000). "Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays." Proc Natl Acad Sci U S A 97(17);9419-24. PMID: 10944214
Krueger90: Krueger S, Zaccai G, Wlodawer A, Langowski J, O'Dea M, Maxwell A, Gellert M (1990). "Neutron and light-scattering studies of DNA gyrase and its complex with DNA." J Mol Biol 211(1);211-20. PMID: 2153834
Lewis96: Lewis RJ, Singh OM, Smith CV, Skarzynski T, Maxwell A, Wonacott AJ, Wigley DB (1996). "The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography." EMBO J 15(6);1412-20. PMID: 8635474
LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532
Loris99: Loris R, Dao-Thi MH, Bahassi EM, Van Melderen L, Poortmans F, Liddington R, Couturier M, Wyns L (1999). "Crystal structure of CcdB, a topoisomerase poison from E. coli." J Mol Biol 285(4);1667-77. PMID: 9917404
MiuraMasuda90: Miura-Masuda A, Ikeda H (1990). "The DNA gyrase of Escherichia coli participates in the formation of a spontaneous deletion by recA-independent recombination in vivo." Mol Gen Genet 220(3);345-52. PMID: 2160049
Mizuuchi80: Mizuuchi K, Fisher LM, O'Dea MH, Gellert M (1980). "DNA gyrase action involves the introduction of transient double-strand breaks into DNA." Proc Natl Acad Sci U S A 77(4);1847-51. PMID: 6246508
Peter04: Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR (2004). "Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli." Genome Biol 5(11);R87. PMID: 15535863
Ruthenburg05: Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL (2005). "A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias." J Biol Chem 280(28);26177-84. PMID: 15897198
Schoeffler10: Schoeffler AJ, May AP, Berger JM (2010). "A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function." Nucleic Acids Res. PMID: 20675723
Sissi05: Sissi C, Marangon E, Chemello A, Noble CG, Maxwell A, Palumbo M (2005). "The effects of metal ions on the structure and stability of the DNA gyrase B protein." J Mol Biol 353(5);1152-60. PMID: 16223508
Smith06: Smith AB, Maxwell A (2006). "A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site." Nucleic Acids Res 34(17);4667-76. PMID: 16963775
Sugino78: Sugino A, Higgins NP, Brown PO, Peebles CL, Cozzarelli NR (1978). "Energy coupling in DNA gyrase and the mechanism of action of novobiocin." Proc Natl Acad Sci U S A 75(10);4838-42. PMID: 368801
Sugino80: Sugino A, Higgins NP, Cozzarelli NR (1980). "DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage." Nucleic Acids Res 8(17);3865-74. PMID: 6255421
Thornton94: Thornton M, Armitage M, Maxwell A, Dosanjh B, Howells AJ, Norris V, Sigee DC (1994). "Immunogold localization of GyrA and GyrB proteins in Escherichia coli." Microbiology 140 ( Pt 9);2371-82. PMID: 7952188
Tsai97: Tsai FT, Singh OM, Skarzynski T, Wonacott AJ, Weston S, Tucker A, Pauptit RA, Breeze AL, Poyser JP, O'Brien R, Ladbury JE, Wigley DB (1997). "The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin." Proteins 28(1);41-52. PMID: 9144789
Cameron11: Cameron AD, Stoebel DM, Dorman CJ (2011). "DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica." Mol Microbiol. PMID: 21276095
Menzel87: Menzel R, Gellert M (1987). "Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters." Proc Natl Acad Sci U S A 84(12);4185-9. PMID: 3035573
Schneider99a: Schneider R, Travers A, Kutateladze T, Muskhelishvili G (1999). "A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli." Mol Microbiol 34(5);953-64. PMID: 10594821
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