GCW_04070

Uniprot: A0A0F6CLJ6
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 439 439 Magnesium 1; catalytic. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 512 512 Magnesium 1; catalytic. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 512 512 Magnesium 2. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 514 514 Magnesium 2. {ECO:0000256|HAMAP-Rule:MF_01898}.
Nucleotide binding:
Site: SITE 464 464 Interaction with DNA. {ECO:0000256|HAMAP-Rule:MF_01898}.; SITE 467 467 Interaction with DNA. {ECO:0000256|HAMAP-Rule:MF_01898}.
Gene names (primary): gyrB
Gene names (synonym):
Mass: 73,758
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 433 547 Toprim. {ECO:0000259|PROSITE:PS50880}.
Motif:
Region:
EMBL: CP006916
ProteinModelPortal:
MEROPS:
EnsemblBacteria KO: AHB99968
UniPathway: K02470
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

In one protein complex with GCW_04065 981126-983073(-)

>nucleotide sequence
TTAGAAGTCAATATTCTTAACTGATTTAGCATTCTTTTCAATGAAGTCACGACGTGGTGA
AACTTCATCACCCATTAGTAGGGAGAATGTCTTATCAGCATTAGCAGCGTCGTTGATTGA
AACTTTTAATAATATTCTCTTCTCTGGATCCATGGTTGTTTCTCAAAGTTGAACATCATC
CATTTCTCCCAGCCCTTTATAACGTTGTAATTCATAACGCACATTTGGATTTTGGTTTTT
TCATTCTTCTAATTGTGCGTCTGAATAAATGTATTTGTTTTGCTTATTGTAGCTAACACG
ATATAAAGGCGGTTGAGCAATATACACATGTCCTTTTTCAATCAATGGAAACATATGTCT
GAAGAAGAACGTTAACAATAAGATCCGAATGTGAGCACCATCGACATCAGCATCGGTCAT
GATGATAATTTTGTTATAACGGATCTTATCAAGTGAAAATTCAGGATTAACACCAGCACC
AATTGCAGTTATTAATGTTCTAATTTCTTCATTTTTAAAGATCTTTTCGTGATTGGCTTT
TTCTACGTTTAACACTTTCCCACGAAGTGGTAAAATAGCTTGATAAAAACGGTCGCGACC
AGATTTAGCTGAACCACCAGCTGAGTCCCCTTCGACGATGTACAGTTCAGAGATCTCCAT
ATCTTTAGTTGTACAATCAGCTAACTTACCTGGTAATGAAGCTGATTCAAAAGGTGATTT
TCTAGCTGATTCTAAAGCTGCTTCAGAACGTTTACGTGAAAACATTGCTGAAACTGCTTT
AGCAGTAATCTTAGCAGCTTCTTCTGGATTTTCTAAGAAAAATCTTTCTAATAGTTCTGA
CACAACACTATTAGTAAACTCTCTTACTTCAGTATTACCTAAACGGTCCTTAGTTTGACC
TTGGTATTGAGGTTCTGAGTGCTTAATTGAGATAATTGCGGTTAAACCTTCACTAAGATC
TTCTTTGCTAATCTTACCGTCAGTTTCTTTAATAAACTTCTTTTCTAACGCATAGCGATT
AATGATCTTATAAAGAGCATTCTTAAACCCTTCTTCATGAGTTCCGCCTTGGTTGGTGTG
AATGTTATTACAGAACGAATAAGTTGAGTTGTAATAACCGTTTGTATATTGAAACGCAAC
TTCTAATAGCATCGTTACTTCTAGATTTCTCTTAGGTAAAGTAACTTTAGTTTTCTTTTC
ACCATAAATGATTTGGGGAATAATTGGTTCTTTAGAAGCATTTAAGTTTTCAACGTATTG
CTTAATTCCACCTTCATATAATCATTCTTGCTTAGTCTTCTTATCAGTTCTTTCATCATT
AAAAATGAATTTTATTCCTTTGTTTAAGAAGGCTAATTGTTCGATCCGATCAGATATGAT
CGTTTCATCGTATTCAAATTGTTCCATGATACTAAAATCTGGAACAAACTGAATTCTTGT
TCCTTGTTTTTTATTATCTGTTCCAATTATTTCTAATGGTTTTAATGAAACCCCACCATC
TTTAAATTCGATGTAATGAATTTTGTAATCGCGATTAACTCAAACTTTGAATGATGAACT
TAAAGCGTTTACTACTGAAGCACCCACCCCATGTAAACCACCTGACATTGAATAAGTATC
GCTATCAAACTTACCACCAGCGTGCAAGATCGTTAAAACAGTTTCAACTGTAGATTTATT
TGTCTTTTCGTGGATGTCAACCGGAATTCCCCGACCATCATCTTCTACTTCAACTAAGTA
GTTATCTTTTAATGTAAGTTTAACAGTTGTTCCATAACCTGCCATCATTTCATCGACAGA
GTTGTCAATGATTTCTCAGATCATATGATGAAGACCTTTTTGATCCGTCGAACCAATATA
CATACCAGGTCTTTTTCGGACAGCTGATAATCCTTCAAGGACCTTAATACTTTGAGAGCT
ATATTGATCTTTTTTTGTGTTGTTCAC

>protein sequence
VNNTKKDQYSSQSIKVLEGLSAVRKRPGMYIGSTDQKGLHHMIWEIIDNSVDEMMAGYGT
TVKLTLKDNYLVEVEDDGRGIPVDIHEKTNKSTVETVLTILHAGGKFDSDTYSMSGGLHG
VGASVVNALSSSFKVWVNRDYKIHYIEFKDGGVSLKPLEIIGTDNKKQGTRIQFVPDFSI
MEQFEYDETIISDRIEQLAFLNKGIKFIFNDERTDKKTKQEWLYEGGIKQYVENLNASKE
PIIPQIIYGEKKTKVTLPKRNLEVTMLLEVAFQYTNGYYNSTYSFCNNIHTNQGGTHEEG
FKNALYKIINRYALEKKFIKETDGKISKEDLSEGLTAIISIKHSEPQYQGQTKDRLGNTE
VREFTNSVVSELLERFFLENPEEAAKITAKAVSAMFSRKRSEAALESARKSPFESASLPG
KLADCTTKDMEISELYIVEGDSAGGSAKSGRDRFYQAILPLRGKVLNVEKANHEKIFKNE
EIRTLITAIGAGVNPEFSLDKIRYNKIIIMTDADVDGAHIRILLLTFFFRHMFPLIEKGH
VYIAQPPLYRVSYNKQNKYIYSDAQLEEWKNQNPNVRYELQRYKGLGEMDDVQLWETTMD
PEKRILLKVSINDAANADKTFSLLMGDEVSPRRDFIEKNAKSVKNIDF