SPM_002500

Uniprot: A0A037UTC8
Description: DNA gyrase subunit B
EC number: 5.99.1.3
Annotation score: 3 out of 5
Miscellaneous [CC]: MISCELLANEOUS: Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. {ECO:0000256|HAMAP-Rule:MF_01898}.
Protein existence: Inferred from homology
Catalytic activity: CATALYTIC ACTIVITY: ATP-dependent breakage, passage and rejoining of double-stranded DNA. {ECO:0000256|HAMAP-Rule:MF_01898, ECO:0000256|SAAS:SAAS00470725}.
Cofactor: COFACTOR: Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000256|HAMAP-Rule:MF_01898}; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000256|HAMAP-Rule:MF_01898}; Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000256|HAMAP-Rule:MF_01898}; ; Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). {ECO:0000256|HAMAP-Rule:MF_01898}
Enzyme regulation:
Function [CC]: FUNCTION: A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner. {ECO:0000256|HAMAP-Rule:MF_01898}.
Pathway:
Active site:
Binding site:
Calcium binding:
DNA binding:
Metal binding: METAL 428 428 Magnesium 1; catalytic. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 501 501 Magnesium 1; catalytic. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 501 501 Magnesium 2. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 503 503 Magnesium 2. {ECO:0000256|HAMAP-Rule:MF_01898}.
Nucleotide binding:
Site: SITE 453 453 Interaction with DNA. {ECO:0000256|HAMAP-Rule:MF_01898}.; SITE 456 456 Interaction with DNA. {ECO:0000256|HAMAP-Rule:MF_01898}.
Gene names (primary): gyrB
Gene names (synonym):
Mass: 72,451
Subunit structure [CC]: SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis. {ECO:0000256|HAMAP-Rule:MF_01898}.
Gene ontology (GO): chromosome [GO:0005694]; cytoplasm [GO:0005737]; ATP binding [GO:0005524]; DNA binding [GO:0003677]; DNA topoisomerase type II (ATP-hydrolyzing) activity [GO:0003918]; magnesium ion binding [GO:0000287]; DNA topological change [GO:0006265]; DNA-dependent DNA replication [GO:0006261]
Gene ontology IDs: GO:0000287; GO:0003677; GO:0003918; GO:0005524; GO:0005694; GO:0005737; GO:0006261; GO:0006265
Chain:
Signal peptide:
Domain [CC]:
Sequence similarities: SIMILARITY: Belongs to the type II topoisomerase family. {ECO:0000256|HAMAP-Rule:MF_01898}.; SIMILARITY: Contains 1 Toprim domain. {ECO:0000256|HAMAP-Rule:MF_01898}.
Protein families: Type II topoisomerase family
Coiled coil:
Domain [FT]: DOMAIN 422 536 Toprim. {ECO:0000259|PROSITE:PS50880}.
Motif:
Region:
EMBL: AGBZ02000001
ProteinModelPortal:
MEROPS:
EnsemblBacteria KO: KAI92885
UniPathway:
CDD:
Gene3D:
HAMAP: 3.30.230.10;3.30.565.10;3.40.50.670
InterPro: MF_01898
PANTHER: IPR002288;IPR011557;IPR003594;IPR020568;IPR014721;IPR001241;IPR013760;IPR013506;IPR013759;IPR018522;IPR006171
PIRSF:
PRINTS:
PROSITE: PR00418
Pfam: PS00177;PS50880
ProDom: PF00204;PF00986;PF02518;PF01751
SMART:
SUPFAM: SM00387;SM00433
TIGRFAMs: SSF54211;SSF55874;SSF56719

468015-469935(+)

>nucleotide sequence
ATGGGTGATAATTATAATTCAGAATCAATTCAAATTTTAGAAGGTTTAGAAGCAGTTCGA
AAACGACCAGGGATGTATATTGGTGCGACAAATGCAAGAGGTTTACATCATTTAGTTTGA
GAAATTGTTGATAACTCAATTGATGAAGTTTTAGCTAATTTTGCTAATAAAATTAAAATT
ATTCTTAATAAGGATGAATCAATTACAGTTATTGATAATGGACGTGGAATTCCAATTGAA
ATTCACCCAAAAACAAAAGTTTCAACATTAGAAACTGTTTTTACTATTTTACATGCAGGA
GGAAAATTTGATTCAAATACATATAAAATTTCTGGAGGTTTACATGGTGTAGGAGCTAGT
GTTGTTAATGCTTTAAGTAAATATTTAAAAGTTGAAGTTAGAAAAAATAATAAAAAATAT
GTAATGGAATTTCATAATGGTGGTCAAATTTTGACACCAATTAAAGAAGTTGGTTCAACT
TCAGAAACTGGAACAACAGTAACTTTTTTACCAGATGAAAAGATTTTTAAAGAAACAACA
ATTTTTAGTTTTTCAACAATTCAAAATCGAATTAAGCAATTAGCTTTTTTAAATAAAGGC
TTAGAAATATCATTAGTTGATTTACGAGAAGAAGATGAAGAAAAAACTGTTCTTTATCAA
TTTAATAATGGAATTAAAGATTATGTTTTAGAACTAAATAAAACAATTGGGACACCATTA
AACGATGTTTTTTATGTGGAAGGAATAGAAGATAATATTGTTGTTGAATTTGGTTTACAA
TATAATGATAATTATTCAGAAAATATTTTCTCTTTTTGTAATAACATTAATACCCATGAA
GGTGGAACTCACGAAGAAGGTGCTAGATTAGCCATTGTTCGTGAAATAAATAATTATTTT
AAAAATATTAATAAAAATAATAAAGGTAATGAAGATAAATTTACTTGAGATGATATTAAA
GAAGGAATGACAATAATAATTTCTATTCGTCATCCTGATCCACAATATGAAGGTCAAACT
AAAACAAAATTAGGAAATAGTGAAGTTAAAAAAATTGTTTCCAATATTGTTGGAAAAGGA
TTAAGTAGTTATTTGTTAGAAAATCCAGAAGATGCAAAAAAAATTATTGAAAAAATAAGT
TTATCGTTAAAAGCAAGAATTGCTGCACAACGTGCAAAAGAAACAACACGTCGTAAGACA
GTTATGGATAGTTTTTCATTACCAGGCAAATTAGCAGATTGTGAAACAAAAGATGCTAAG
ATAGCTGAACTTTATATTGTCGAAGGAGATTCTGCTGGTGGAAGTGCTAAATCGGGACGA
AATCGAAAATTTCAAGCAATTTTACCGTTACGAGGAAAAATTTTAAATGTGGAAAAAGCA
AAACAAATAAAAATATTTGAAAATAATGAAATTAATTCAATTATTACCGCATTAGGAGCA
GGTATTAAAGATAATTTTAATGATAAAAAATTACGTTATCAAAAGGTAATCATTATGACT
GATGCTGATGTTGATGGCGCACATATACGAATTTTACTATTAACATTTTTTTATCGTTAT
ATGAAAGATTTAATTGAAAATGGCAATATTTATATTGCTCAACCACCATTATATAAAATA
CAAAATGGTAATCAGATTCGATATGCTTATAGTGATAATGAATTAGAACTTTATAAAGAA
GAATTATTAAAACAAAATAAAAATTATACAATTCAACGTTATAAAGGTTTAGGAGAAATG
AATCCAGAACAATTATGAGAAACAACAATGAATCCAGAACGGCGTTTATTACTGAAAGTT
TCTGTTAATAATGCATTTGAAGCAAATTTAATTTGTAATGAATTAATGGGTGAAAATGTT
GAACCACGGAAAAAATTTATTCGTGAAAATGCAAAATATGTTAAAAATTTAGATGTCTAG

>protein sequence
MGDNYNSESIQILEGLEAVRKRPGMYIGATNARGLHHLVWEIVDNSIDEVLANFANKIKI
ILNKDESITVIDNGRGIPIEIHPKTKVSTLETVFTILHAGGKFDSNTYKISGGLHGVGAS
VVNALSKYLKVEVRKNNKKYVMEFHNGGQILTPIKEVGSTSETGTTVTFLPDEKIFKETT
IFSFSTIQNRIKQLAFLNKGLEISLVDLREEDEEKTVLYQFNNGIKDYVLELNKTIGTPL
NDVFYVEGIEDNIVVEFGLQYNDNYSENIFSFCNNINTHEGGTHEEGARLAIVREINNYF
KNINKNNKGNEDKFTWDDIKEGMTIIISIRHPDPQYEGQTKTKLGNSEVKKIVSNIVGKG
LSSYLLENPEDAKKIIEKISLSLKARIAAQRAKETTRRKTVMDSFSLPGKLADCETKDAK
IAELYIVEGDSAGGSAKSGRNRKFQAILPLRGKILNVEKAKQIKIFENNEINSIITALGA
GIKDNFNDKKLRYQKVIIMTDADVDGAHIRILLLTFFYRYMKDLIENGNIYIAQPPLYKI
QNGNQIRYAYSDNELELYKEELLKQNKNYTIQRYKGLGEMNPEQLWETTMNPERRLLLKV
SVNNAFEANLICNELMGENVEPRKKFIRENAKYVKNLDV