ACL_RS00035

Uniprot: A9NE69
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 427 427 Magnesium 1; catalytic. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 500 500 Magnesium 1; catalytic. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 500 500 Magnesium 2. {ECO:0000256|HAMAP-Rule:MF_01898}.; METAL 502 502 Magnesium 2. {ECO:0000256|HAMAP-Rule:MF_01898}.
Nucleotide binding:
Site: SITE 452 452 Interaction with DNA. {ECO:0000256|HAMAP-Rule:MF_01898}.; SITE 455 455 Interaction with DNA. {ECO:0000256|HAMAP-Rule:MF_01898}.
Gene names (primary): gyrB
Gene names (synonym):
Mass: 71,215
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 421 535 Toprim. {ECO:0000259|PROSITE:PS50880}.
Motif:
Region:
EMBL: CP000896
ProteinModelPortal: A9NE69
MEROPS:
EnsemblBacteria KO: ABX80649
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

5728-7636(+)

>nucleotide sequence
ATGCCAAATAATAATAACAGTCATTATACTGCAGATAATATTCAAATATTGGAAGGATTA
GAAGCAGTTAAAAAAAGACCAGGTATGTATATCGGATCCACAGGTGAACGTGGACTTCAC
CACTTAGTTTGGGAAATCGTTGATAACTCAATTGACGAGGCTTTAGGCGGATATGCAGAT
GAAATCACCATAGAGATTTTAAAAGGTGAAGTGATACGCGTTACTGATAATGGTCGTGGT
ATTCCAGTAGATATCCACCCTAAGACAAAAAGACCAGCTGTTGAAACGATTTTAACAACG
CTTCATGCAGGTGGTAAGTTTGATAAAGGTTCTTATAAAGTTTCTGGTGGTCTACACGGT
GTAGGGGCATCTGTAGTCAACGGTTTATCTGAATGGTTTGTTGTAGAAATTCATAAAGAT
GGAACGATTTATGAACAAAAATATGAACGTGGTATTCCAGCATATGACCTTAAAGTAAAA
GGAAGTACAGATAAATCAGGAACGATTATTTCATTCCAAGCGGATCCACTTATTTTTACT
GAAACAGTTATTTATAACTATGAAACATTAAGAACAAGAATCCAACAATTAGCATTCTTA
AATAAAGGACTTAAACTGAATTTAATCGATGATCGTTTTGAAGAAAACAAGTCTGAATCA
TTCCACTACGAAGGTGGTATTACAGAATATGTTAAGTTCTTAAATCAGTCTAAATCAAAG
ATTCATAATGACATTATTTATATCGATAAAGAACAAGATGGCATCACGGTAGAACTTGCT
ATGCAGTTTGTAGATAGCTATTCTCCAAACCTACATTCATTTACAAATAACATCTCAACT
ACTGAAGGTGGAATGCACGAAGATGGCTTCAAGATGGCATTAACGCGTGTTATATCTAAG
TATGCAGATGATTTAAAAATGAAAAAAGATGACAGTATTTCAGGTGAGGATACTAGAGAA
GGTTTAACTGCAATTATTTCAGTTAAACACCCTGAACCTCAATTTGAAGGACAAACAAAA
ACTAAATTAGGTAACCCTGAAGTTCGTGCAATTACATCCCAAATTACTAGTGAAGCCATA
GAACGTTTTTTAATGGAAAATCCAGCTCAAGCAAAAGCGATTGTTGAAAAAGTTTTACTT
GCAACACGCGCACGTGTTGCTGCAAGAAAAGCAAAAGATTTAACAAGAAGAAAATCACCA
CTTGATGCTTTAGGATTTGCAAGTAAACTAGCGGATTGCCGCAGTAAAGATCCTGAAAAA
TCAGAAATCTATATTGTGGAAGGGGACTCTGCGGGTGGTTCTGCAAAACAAGGTAGAGAC
TCAGAATTCCAAGCAATTATGCCATTACGTGGTAAGGTCTTAAACGTAGAAAAAGCACGT
CTAGATAAAATGCTTTCTAATAAAGAAATTGTGAACTTAATCCAAGCTATGGGTACAGGT
ATCTCTGATGAGTTTGATATTACCAAAGCACGTTATCATAAAATTGTTATTATGACCGAT
GCTGACGTCGACGGTGCACATATTAGAACCCTACTATTAACATTCTTATTTAGACATATG
AGACCATTAATTGATGCTGGTTATGTATATGCAGCTCAACCACCACTATATAAAATTTCT
TGGGGCAGAAATTTTCAATATGCTTATAATGAACAAGAATTAAATGAACTACTAAAAACA
ATAGAAACAAAACCATCTATTCAACGTTATAAAGGTTTAGGAGAAATGGATGCTGAGCAA
TTATGGGATACTACAATGGATCCTGCAAAGCGTACTTTACTTCAAATTAAATTAGAAGAT
GCTATCGAAGCCGATCAAGTGTTTTCTATGTTAATGGGTGAAGAAGTTGAACCAAGAAAA
GAATTTATTCAAAATAATGCACAATATGCAACAGATATTGACGCATAG

>protein sequence
MPNNNNSHYTADNIQILEGLEAVKKRPGMYIGSTGERGLHHLVWEIVDNSIDEALGGYAD
EITIEILKGEVIRVTDNGRGIPVDIHPKTKRPAVETILTTLHAGGKFDKGSYKVSGGLHG
VGASVVNGLSEWFVVEIHKDGTIYEQKYERGIPAYDLKVKGSTDKSGTIISFQADPLIFT
ETVIYNYETLRTRIQQLAFLNKGLKLNLIDDRFEENKSESFHYEGGITEYVKFLNQSKSK
IHNDIIYIDKEQDGITVELAMQFVDSYSPNLHSFTNNISTTEGGMHEDGFKMALTRVISK
YADDLKMKKDDSISGEDTREGLTAIISVKHPEPQFEGQTKTKLGNPEVRAITSQITSEAI
ERFLMENPAQAKAIVEKVLLATRARVAARKAKDLTRRKSPLDALGFASKLADCRSKDPEK
SEIYIVEGDSAGGSAKQGRDSEFQAIMPLRGKVLNVEKARLDKMLSNKEIVNLIQAMGTG
ISDEFDITKARYHKIVIMTDADVDGAHIRTLLLTFLFRHMRPLIDAGYVYAAQPPLYKIS
WGRNFQYAYNEQELNELLKTIETKPSIQRYKGLGEMDAEQLWDTTMDPAKRTLLQIKLED
AIEADQVFSMLMGEEVEPRKEFIQNNAQYATDIDA