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Escherichia coli K-12 substr. MG1655 Polypeptide: DNA gyrase, subunit A



Gene: gyrA Accession Numbers: EG10423 (EcoCyc), b2231, ECK2223

Synonyms: hisW, nalA, nfxA, norA, parD

Regulation Summary Diagram: ?

Component of: DNA gyrase (extended summary available)

Gene Citations: [Neumann97]

Locations: bacterial nucleoid, cytosol, membrane

Map Position: [2,334,815 <- 2,337,442] (50.32 centisomes)
Length: 2628 bp / 875 aa

Molecular Weight of Polypeptide: 96.963 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007370 , CGSC:651 , DIP:DIP-36179N , EchoBASE:EB0418 , EcoGene:EG10423 , EcoliWiki:b2231 , Mint:MINT-201682 , ModBase:P0AES4 , OU-Microarray:b2231 , PortEco:gyrA , PR:PRO_000022855 , Pride:P0AES4 , Protein Model Portal:P0AES4 , RefSeq:NP_416734 , RegulonDB:EG10423 , SMR:P0AES4 , String:511145.b2231 , Swiss-Model:P0AES4 , UniProt:P0AES4

Relationship Links: InterPro:IN-FAMILY:IPR002205 , InterPro:IN-FAMILY:IPR005743 , InterPro:IN-FAMILY:IPR006691 , InterPro:IN-FAMILY:IPR013757 , InterPro:IN-FAMILY:IPR013758 , InterPro:IN-FAMILY:IPR013760 , InterPro:IN-FAMILY:IPR024946 , PDB:Structure:1AB4 , PDB:Structure:1X75 , PDB:Structure:1ZI0 , PDB:Structure:2Y3P , PDB:Structure:3NUH , PDB:Structure:4ELY , Pfam:IN-FAMILY:PF00521 , Pfam:IN-FAMILY:PF03989 , Smart:IN-FAMILY:SM00434

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred by computational analysis Inferred from experiment [Maxwell84, Sugino78, Gellert76, GOA06, GOA01, GOA01a]
GO:0006265 - DNA topological change Inferred from experiment Inferred by computational analysis [GOA01a, Steck84]
GO:0006351 - transcription, DNA-templated Inferred from experiment [Higgins78a, Peter04]
GO:0042493 - response to drug Inferred from experiment [Staudenbauer76, Chao82, Bourguignon73]
GO:0006259 - DNA metabolic process Inferred by computational analysis [GOA01a]
GO:0006261 - DNA-dependent DNA replication Inferred by computational analysis [GOA06]
GO:0006268 - DNA unwinding involved in DNA replication Inferred by computational analysis [Gaudet10]
GO:0007059 - chromosome segregation Inferred by computational analysis [Gaudet10]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Higgins82, Reece91]
GO:0003918 - DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Gellert76, Sugino78]
GO:0005515 - protein binding Inferred from experiment [Domain09, Butland05]
GO:0008094 - DNA-dependent ATPase activity Inferred from experiment [Maxwell84]
GO:0042802 - identical protein binding Inferred from experiment [Lasserre06, Rajagopala09]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003916 - DNA topoisomerase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, Thornton94, Lasserre06]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005694 - chromosome Inferred by computational analysis [GOA01a]
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
information transfer RNA related Transcription related

Essentiality data for gyrA knockouts: ?

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

Subunit composition of DNA gyrase = [GyrA]2[GyrB]2
         DNA gyrase, subunit A = GyrA
         DNA gyrase, subunit B = GyrB (summary available)

Summary:
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 activity is required for DNA synthesis and replication fork progression [Fairweather80, Khodursky00, Smelkova01].

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, Smith06a]. A crystal structure of CcdB has been determined [Loris99].

Gyrase supercoiling activity is regulated by the inhibitor protein GyrI; for more information, see DNA gyrase inhibitor. Glutamate racemase also modulates gyrase supercoiling activity [Ashiuchi02].

Locations: cytosol

GO Terms:

Cellular Component: GO:0005829 - cytosol

Credits:
Last-Curated ? 20-Mar-2006 by Shearer A , SRI International


Enzymatic reaction of: gyrase

EC Number: 5.99.1.3

a double stranded DNA + ATP <=> a negatively supercoiled DNA + ADP + phosphate

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.

Cofactors or Prosthetic Groups: Mg2+ [Gellert76]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
300.0
[Higgins78a]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt11]
UniProt: Removed.
Chain 2 -> 875
[UniProt11]
UniProt: DNA gyrase subunit A.
Mutagenesis-Variant 32
[Hockings02, UniProt13]
Alternate sequence: R → Q; UniProt: Nearly abolishes DNA supercoiling. Reduces DNA cleavage and relaxation.
Alternate sequence: R → A; UniProt: Nearly abolishes DNA supercoiling. Reduces DNA cleavage and relaxation.
Active-Site 32, 47, 78, 80
[Hockings02]
These residues are involved in the cleavage but not the religation portion of the cleavage-religation reaction.
Mutagenesis-Variant 47
[Hockings02, UniProt13]
Alternate sequence: R → Q; UniProt: Nearly abolishes DNA supercoiling. Reduces DNA cleavage. Slightly reduces DNA relaxation.
Extrinsic-Sequence-Variant 67
[UniProt10a]
Alternate sequence: A → S; UniProt: (in PPA-10; quinolone-resistant);
Mutagenesis-Variant 78
[Hockings02, UniProt13]
Alternate sequence: H → A; UniProt: Nearly abolishes DNA supercoiling. Reduces DNA cleavage and DNA relaxation.
Mutagenesis-Variant 80
[Hockings02, UniProt13]
Alternate sequence: H → A; UniProt: Reduces DNA supercoiling. Slightly reduces DNA cleavage. No effect on DNA relaxation.
Extrinsic-Sequence-Variant 81
[UniProt10a]
Alternate sequence: G → C; UniProt: (in NAL-97; quinolone-resistant);
Mutagenesis-Variant 83
[Hallett91, UniProt11a]
Alternate sequence: S → A; UniProt: Resistant to fluoroquinolones.
Extrinsic-Sequence-Variant 83
[UniProt10a]
Alternate sequence: S → W; UniProt: (in PPA-18 and strain 227; quinolone-resistant);
Alternate sequence: S → L; UniProt: (in NAL-51, NAL-112, NAL-118 and NAL-119; quinolone-resistant);
Extrinsic-Sequence-Variant 84
[UniProt10a]
Alternate sequence: A → P; UniProt: (in PPA-05; quinolone-resistant);
Extrinsic-Sequence-Variant 87
[UniProt10a]
Alternate sequence: D → V; UniProt: (in strain: 202; quinolone- resistant);
Alternate sequence: D → N; UniProt: (in NAL-113 and KL-16; quinolone- resistant);
Mutagenesis-Variant 106
[Hallett91, UniProt11a]
Alternate sequence: Q → R; UniProt: Resistant to fluoroquinolones.
Extrinsic-Sequence-Variant 106
[UniProt10a]
Alternate sequence: Q → H; UniProt: (in NAL-89; quinolone-resistant);
Active-Site 122
[Horowitz87]
This is the tyrosine that becomes bound to the 5' end of the target DNA during the cleavage-religation reaction.
Mutagenesis-Variant 462
[Bernard93, Bernard92, UniProt11]
Alternate sequence: R → C; UniProt: In gyrA462; resistant to cytotoxic protein CcdB, but not to the quinoline antibiotic enoxacin, has no effect on DNA supercoiling. Does not interact with CcdB.
Extrinsic-Sequence-Variant 678
[UniProt10a]
Alternate sequence: D → E; UniProt: (in strain: 227);
Extrinsic-Sequence-Variant 798
[UniProt10a]
Alternate sequence: I → IMMI; UniProt: (in KL-16; quinolone- resistant);
Extrinsic-Sequence-Variant 828
[UniProt10a]
Alternate sequence: A → S; UniProt: (in strain: 227);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2231 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10423; confirmed by SwissProt match.


References

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

Ashiuchi02: Ashiuchi M, Kuwana E, Yamamoto T, Komatsu K, Soda K, Misono H (2002). "Glutamate racemase is an endogenous DNA gyrase inhibitor." J Biol Chem 277(42);39070-3. PMID: 12213801

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

Bernard92: Bernard P, Couturier M (1992). "Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes." J Mol Biol 226(3);735-45. PMID: 1324324

Bernard93: Bernard P, Kezdy KE, Van Melderen L, Steyaert J, Wyns L, Pato ML, Higgins PN, Couturier M (1993). "The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase." J Mol Biol 234(3);534-41. PMID: 8254658

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

Bourguignon73: Bourguignon GJ, Levitt M, Sternglanz R (1973). "Studies on the mechanism of action of nalidixic acid." Antimicrob Agents Chemother 4(4);479-86. PMID: 4208771

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

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

Chao82: Chao L, Tillman DM (1982). "Enhanced resistance to nitrosoguanidine killing and mutagenesis in a DNA gyrase mutant of Escherichia coli." J Bacteriol 151(2);764-70. PMID: 6178722

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

Cullis92: Cullis PM, Maxwell A, Weiner DP (1992). "Energy coupling in DNA gyrase: a thermodynamic limit to the extent of DNA supercoiling." Biochemistry 31(40);9642-6. PMID: 1327123

DaoThi05: Dao-Thi MH, Van Melderen L, De Genst E, Afif H, Buts L, Wyns L, Loris R (2005). "Molecular basis of gyrase poisoning by the addiction toxin CcdB." J Mol Biol 348(5);1091-102. PMID: 15854646

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

Domain09: Domain F, Levy SB (2009). "GyrA Interacts with MarR to Reduce Repression of the marRAB Operon in E. coli." J Bacteriol. PMID: 19933356

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

Fisher81: Fisher LM, Mizuuchi K, O'Dea MH, Ohmori H, Gellert M (1981). "Site-specific interaction of DNA gyrase with DNA." Proc Natl Acad Sci U S A 78(7);4165-9. PMID: 6270661

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

Gellert76: Gellert M, Mizuuchi K, O'Dea MH, Nash HA (1976). "DNA gyrase: an enzyme that introduces superhelical turns into DNA." Proc Natl Acad Sci U S A 73(11);3872-6. PMID: 186775

Gellert79: Gellert M, Fisher LM, O'Dea MH (1979). "DNA gyrase: purification and catalytic properties of a fragment of gyrase B protein." Proc Natl Acad Sci U S A 76(12);6289-93. PMID: 230505

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."

Gore06: Gore J, Bryant Z, Stone MD, Nollmann M, Cozzarelli NR, Bustamante C (2006). "Mechanochemical analysis of DNA gyrase using rotor bead tracking." Nature 439(7072);100-4. PMID: 16397501

Hallett91: Hallett P, Maxwell A (1991). "Novel quinolone resistance mutations of the Escherichia coli DNA gyrase A protein: enzymatic analysis of the mutant proteins." Antimicrob Agents Chemother 35(2);335-40. PMID: 1850970

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

Higgins82: Higgins NP, Cozzarelli NR (1982). "The binding of gyrase to DNA: analysis by retention by nitrocellulose filters." Nucleic Acids Res 10(21);6833-47. PMID: 6294616

Hockings02: Hockings SC, Maxwell A (2002). "Identification of four GyrA residues involved in the DNA breakage-reunion reaction of DNA gyrase." J Mol Biol 318(2);351-9. PMID: 12051842

Horowitz87: Horowitz DS, Wang JC (1987). "Mapping the active site tyrosine of Escherichia coli DNA gyrase." J Biol Chem 262(11);5339-44. PMID: 3031051

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

Kampranis99: Kampranis SC, Bates AD, Maxwell A (1999). "A model for the mechanism of strand passage by DNA gyrase." Proc Natl Acad Sci U S A 96(15);8414-9. PMID: 10411889

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

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

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

Marians87: Marians KJ (1987). "DNA gyrase-catalyzed decatenation of multiply linked DNA dimers." J Biol Chem 262(21);10362-8. PMID: 3038875

Maxwell84: Maxwell A, Gellert M (1984). "The DNA dependence of the ATPase activity of DNA gyrase." J Biol Chem 259(23);14472-80. PMID: 6094559

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

Morais97: Morais Cabral JH, Jackson AP, Smith CV, Shikotra N, Maxwell A, Liddington RC (1997). "Crystal structure of the breakage-reunion domain of DNA gyrase." Nature 388(6645);903-6. PMID: 9278055

Morrison79: Morrison A, Cozzarelli NR (1979). "Site-specific cleavage of DNA by E. coli DNA gyrase." Cell 17(1);175-84. PMID: 378403

Neumann97: Neumann S, Quinones A (1997). "Discoordinate gene expression of gyrA and gyrB in response to DNA gyrase inhibition in Escherichia coli." J Basic Microbiol 1997;37(1);53-69. PMID: 9090126

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

Rajagopala09: Rajagopala SV, Hughes KT, Uetz P (2009). "Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins." Proteomics 9(23);5296-302. PMID: 19834901

Reece91: Reece RJ, Maxwell A (1991). "The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein." Nucleic Acids Res 19(7);1399-405. PMID: 1851291

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

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

Smelkova01: Smelkova N, Marians KJ (2001). "Timely release of both replication forks from oriC requires modulation of origin topology." J Biol Chem 276(42);39186-91. PMID: 11504719

Smith06a: 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

Staudenbauer76: Staudenbauer WL (1976). "Replication of Escherichia coli DNA in vitro: inhibition by oxolinic acid." Eur J Biochem 62(3);491-7. PMID: 770163

Steck84: Steck TR, Pruss GJ, Manes SH, Burg L, Drlica K (1984). "DNA supercoiling in gyrase mutants." J Bacteriol 158(2);397-403. PMID: 6327603

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

Sugino80a: Sugino A, Cozzarelli NR (1980). "The intrinsic ATPase of DNA gyrase." J Biol Chem 255(13);6299-306. PMID: 6248518

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt11a: 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.

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."

Wigley91: Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G (1991). "Crystal structure of an N-terminal fragment of the DNA gyrase B protein." Nature 351(6328);624-9. PMID: 1646964

Williams01: Williams NL, Howells AJ, Maxwell A (2001). "Locking the ATP-operated clamp of DNA gyrase: probing the mechanism of strand passage." J Mol Biol 306(5);969-84. PMID: 11237612

Williams99a: Williams NL, Maxwell A (1999). "Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking." Biochemistry 38(41);13502-11. PMID: 10521257

Yang88: Yang Y, Ames GF (1988). "DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences." Proc Natl Acad Sci U S A 85(23);8850-4. PMID: 2848243

Other References Related to Gene Regulation

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

GomezGomez96: Gomez-Gomez JM, Baquero F, Blazquez J (1996). "Cyclic AMP receptor protein positively controls gyrA transcription and alters DNA topology after nutritional upshift in Escherichia coli." J Bacteriol 1996;178(11);3331-4. PMID: 8655515

Jones92: Jones PG, Krah R, Tafuri SR, Wolffe AP (1992). "DNA gyrase, CS7.4, and the cold shock response in Escherichia coli." J Bacteriol 1992;174(18);5798-802. PMID: 1325964

Mitchell03: Mitchell JE, Zheng D, Busby SJ, Minchin SD (2003). "Identification and analysis of 'extended -10' promoters in Escherichia coli." Nucleic Acids Res 31(16);4689-95. PMID: 12907708

Schneider99: 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

Swanberg87: Swanberg SL, Wang JC (1987). "Cloning and sequencing of the Escherichia coli gyrA gene coding for the A subunit of DNA gyrase." J Mol Biol 197(4);729-36. PMID: 2828631


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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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