DNA gyrase subunit B
Details
- Name
- DNA gyrase subunit B
- Synonyms
- 5.99.1.3
- acrB
- himB
- hisU
- nalC
- parA
- pcbA
- Gene Name
- gyrB
- UniProtKB Entry
- P0AES6Swiss-Prot
- Organism
- Escherichia coli (strain K12)
- NCBI Taxonomy ID
- 83333
- Amino acid sequence
>lcl|BSEQ0016210|DNA gyrase subunit B MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEII VTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGV SVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVT EFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNI FYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKE GYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEY LLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSEL YLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGR DEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKG KQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERR YPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLF EPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFE QALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTL MGDAVEPRRAFIEENALKAANIDI
- Number of residues
- 804
- Molecular Weight
- 89949.195
- Theoretical pI
- 5.93
- GO Classification
- FunctionsATP binding / DNA binding / DNA topoisomerase type II (ATP-hydrolyzing) activity / DNA-dependent ATPase activity / magnesium ion bindingProcessesDNA topological change / DNA-dependent DNA replication / response to antibiotic / response to drug / transcription, DNA-templatedComponentschromosome / cytoplasm / cytosol / DNA topoisomerase complex (ATP-hydrolyzing)
- General Function
- DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner to maintain chromosomes in an underwound state (PubMed:12051842, PubMed:12051843, PubMed:1323022, PubMed:18642932, PubMed:186775, PubMed:19060136, PubMed:19965760, PubMed:20356737, PubMed:20675723, PubMed:22457353, PubMed:23294697, PubMed:23352267, PubMed:24386374, PubMed:25202966, PubMed:25849408, PubMed:3031051, PubMed:7811004, PubMed:8248233, PubMed:8621650, PubMed:9657678). This makes better substrates for topoisomerase 4 (ParC and ParE) which is the main enzyme that unlinks newly replicated chromosomes in E.coli (PubMed:9334322). Gyrase catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:22457352). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:337300). E.coli gyrase has higher supercoiling activity than other characterized bacterial gyrases; at comparable concentrations E.coli gyrase introduces more supercoils faster than M.tuberculosis gyrase, while M.tuberculosis gyrase has higher decatenation than supercoiling activity compared to E.coli (PubMed:22457352). E.coli makes 15% more negative supercoils in pBR322 plasmid DNA than S.typhimurium; the S.typhimurium GyrB subunit is toxic in E.coli, while the E.coli copy can be expressed in S.typhimurium even though the 2 subunits have 777/804 residues identical (PubMed:17400739). The enzymatic differences between E.coli gyrase and topoisomerase IV are largely due to the GyrA C-terminal domain (approximately residues 524-841) and specifically the GyrA-box (PubMed:16332690, PubMed:8962066).
- Specific Function
- ATP binding
- Pfam Domain Function
- Signal Regions
- Not Available
- Transmembrane Regions
- Not Available
- Cellular Location
- Cytoplasm
- Gene sequence
>lcl|BSEQ0016211|DNA gyrase subunit B (gyrB) ATGTCGAATTCTTATGACTCCTCCAGTATCAAAGTCCTGAAAGGGCTGGATGCGGTGCGT AAGCGCCCGGGTATGTATATCGGCGACACGGATGACGGCACCGGTCTGCACCACATGGTA TTCGAGGTGGTAGATAACGCTATCGACGAAGCGCTCGCGGGTCACTGTAAAGAAATTATC GTCACCATTCACGCCGATAACTCTGTCTCTGTACAGGATGACGGGCGCGGCATTCCGACC GGTATTCACCCGGAAGAGGGCGTATCGGCGGCGGAAGTGATCATGACCGTTCTGCACGCA GGCGGTAAATTTGACGATAACTCCTATAAAGTGTCCGGCGGTCTGCACGGCGTTGGTGTT TCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTTATCCAGCGCGAGGGTAAAATT CACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCGCTGGCGGTTACCGGCGAGACT GAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTCGAAACCTTCACCAATGTGACC GAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAGTTGTCGTTCCTCAACTCCGGC GTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAAGACCACTTCCACTATGAAGGC GGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAAACGCCGATCCACCCGAATATC TTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAAGTGGCGTTGCAGTGGAACGAT GGCTTCCAGGAAAACATCTACTGCTTTACCAACAACATTCCGCAGCGTGACGGCGGTACT CACCTGGCAGGCTTCCGTGCGGCGATGACCCGTACCCTGAACGCCTACATGGACAAAGAA GGCTACAGCAAAAAAGCCAAAGTCAGCGCCACCGGTGACGATGCGCGTGAAGGCCTGATT GCGGTCGTTTCCGTGAAAGTGCCGGACCCGAAATTCTCCTCCCAGACCAAAGACAAACTG GTTTCTTCTGAGGTGAAATCGGCGGTTGAACAGCAGATGAACGAACTGCTGGCAGAATAC CTGCTGGAAAACCCAACCGACGCGAAAATCGTGGTTGGCAAAATTATCGATGCTGCCCGT GCCCGTGAAGCGGCGCGTCGCGCGCGTGAAATGACCCGCCGTAAAGGTGCGCTCGACTTA GCGGGCCTGCCGGGCAAACTGGCAGACTGCCAGGAACGCGATCCGGCGCTTTCCGAACTG TACCTGGTGGAAGGGGACTCCGCGGGCGGCTCTGCGAAGCAGGGGCGTAACCGCAAGAAC CAGGCGATTCTGCCGCTGAAGGGTAAAATCCTCAACGTCGAGAAAGCGCGCTTCGATAAG ATGCTCTCTTCTCAGGAAGTGGCGACGCTTATCACCGCGCTTGGCTGTGGTATCGGTCGT GACGAGTACAACCCGGACAAACTGCGTTATCACAGCATCATCATCATGACCGATGCGGAC GTCGACGGCTCGCACATTCGTACGCTGCTGTTGACCTTCTTCTATCGTCAGATGCCGGAA ATCGTTGAACGCGGTCACGTCTACATCGCTCAGCCGCCGCTGTACAAAGTGAAGAAAGGC AAGCAGGAACAGTACATTAAAGACGACGAAGCGATGGATCAGTACCAGATCTCTATCGCG CTGGACGGCGCAACGCTGCACACCAACGCCAGTGCACCGGCATTGGCTGGCGAAGCGTTA GAGAAACTGGTATCTGAGTACAACGCGACGCAGAAAATGATCAATCGTATGGAGCGTCGT TATCCGAAAGCAATGCTGAAAGAGCTTATCTATCAGCCGACGTTGACGGAAGCTGACCTT TCTGATGAGCAGACCGTTACCCGCTGGGTGAACGCGCTGGTCAGCGAACTGAACGACAAA GAACAGCACGGCAGCCAGTGGAAGTTTGATGTTCACACCAATGCTGAGCAAAACCTGTTC GAGCCGATTGTTCGCGTGCGTACCCACGGTGTGGATACTGACTATCCGCTGGATCACGAG TTTATCACCGGTGGCGAATATCGTCGTATCTGCACGCTGGGTGAGAAACTGCGTGGCTTG CTGGAAGAAGATGCGTTTATCGAACGTGGCGAGCGTCGTCAGCCGGTAGCCAGCTTCGAG CAGGCGCTGGACTGGCTGGTGAAAGAGTCCCGTCGCGGCCTCTCCATCCAGCGTTATAAA GGTCTGGGCGAGATGAACCCGGAACAGCTGTGGGAAACCACTATGGACCCGGAAAGTCGT CGTATGCTGCGCGTTACCGTTAAAGATGCGATTGCTGCCGACCAGTTGTTCACCACGCTG ATGGGCGACGCCGTTGAACCGCGCCGTGCGTTTATTGAAGAGAACGCCCTGAAAGCGGCG AATATCGATATTTAA
- Chromosome Location
- Not Available
- Locus
- Not Available
- External Identifiers
Resource Link UniProtKB ID P0AES6 UniProtKB Entry Name GYRB_ECOLI GenBank Protein ID 41646 GenBank Gene ID X04341 PDB ID(s) 1AJ6, 1EI1, 1KZN, 3G7E, 3NUH, 4DUH, 4HYP, 4KFG, 4PRV, 4PRX, 4PU9, 4WUB, 4WUC, 4WUD, 4XTJ, 4ZVI KEGG ID ecj:JW5625 NCBI Gene ID 948211 - General References
- Yamagishi J, Yoshida H, Yamayoshi M, Nakamura S: Nalidixic acid-resistant mutations of the gyrB gene of Escherichia coli. Mol Gen Genet. 1986 Sep;204(3):367-73. [Article]
- Adachi T, Mizuuchi M, Robinson EA, Appella E, O'Dea MH, Gellert M, Mizuuchi K: DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy. Nucleic Acids Res. 1987 Jan 26;15(2):771-84. [Article]
- Funatsuki K, Tanaka R, Inagaki S, Konno H, Katoh K, Nakamura H: acrB mutation located at carboxyl-terminal region of gyrase B subunit reduces DNA binding of DNA gyrase. J Biol Chem. 1997 May 16;272(20):13302-8. [Article]
- Burland V, Plunkett G 3rd, Daniels DL, Blattner FR: DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics. 1993 Jun;16(3):551-61. [Article]
- Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. [Article]
- Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL: Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res. 2006 Jan 5;34(1):1-9. Print 2006. [Article]
- Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. Epub 2006 Feb 21. [Article]
- Adachi T, Mizuuchi K, Menzel R, Gellert M: DNA sequence and transcription of the region upstream of the E. coli gyrB gene. Nucleic Acids Res. 1984 Aug 24;12(16):6389-95. [Article]
- Menzel R, Gellert M: Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment. J Bacteriol. 1987 Mar;169(3):1272-8. [Article]
- Tamura JK, Gellert M: Characterization of the ATP binding site on Escherichia coli DNA gyrase. Affinity labeling of Lys-103 and Lys-110 of the B subunit by pyridoxal 5'-diphospho-5'-adenosine. J Biol Chem. 1990 Dec 5;265(34):21342-9. [Article]
- Vizan JL, Hernandez-Chico C, del Castillo I, Moreno F: The peptide antibiotic microcin B17 induces double-strand cleavage of DNA mediated by E. coli DNA gyrase. EMBO J. 1991 Feb;10(2):467-76. [Article]
- VanBogelen RA, Abshire KZ, Moldover B, Olson ER, Neidhardt FC: Escherichia coli proteome analysis using the gene-protein database. Electrophoresis. 1997 Aug;18(8):1243-51. [Article]
- Noble CG, Maxwell A: The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J Mol Biol. 2002 Apr 26;318(2):361-71. [Article]
- Sissi C, Chemello A, Vazquez E, Mitchenall LA, Maxwell A, Palumbo M: DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action. Biochemistry. 2008 Aug 19;47(33):8538-45. doi: 10.1021/bi800480j. Epub 2008 Jul 22. [Article]
- Schoeffler AJ, May AP, Berger JM: A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res. 2010 Nov;38(21):7830-44. doi: 10.1093/nar/gkq665. Epub 2010 Jul 31. [Article]
- Brvar M, Perdih A, Renko M, Anderluh G, Turk D, Solmajer T: Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors. J Med Chem. 2012 Jul 26;55(14):6413-26. doi: 10.1021/jm300395d. Epub 2012 Jul 5. [Article]
- Yoshida H, Bogaki M, Nakamura M, Yamanaka LM, Nakamura S: Quinolone resistance-determining region in the DNA gyrase gyrB gene of Escherichia coli. Antimicrob Agents Chemother. 1991 Aug;35(8):1647-50. [Article]
- Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G: Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature. 1991 Jun 20;351(6328):624-9. [Article]
- Holdgate GA, Tunnicliffe A, Ward WH, Weston SA, Rosenbrock G, Barth PT, Taylor IW, Pauptit RA, Timms D: The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study. Biochemistry. 1997 Aug 12;36(32):9663-73. [Article]
Associated Data
- Bio-Entities
Bio-Entity Type DNA gyrase subunit B (Escherichia coli (strain K12)) protein primary- Drug Relations
Drug Drug group Pharmacological action? Type Actions Details Rosoxacin approved, investigational yes target inhibitor Details Phosphoaminophosphonic Acid-Adenylate Ester experimental unknown target Details Clorobiocin experimental unknown target Details Technetium Tc-99m ciprofloxacin investigational unknown target Details Coumermycin A1 experimental yes target inhibitor Details Fobrepodacin investigational yes target inhibitor Details