Q5F5Z6 · GYRB_NEIG1
- ProteinDNA gyrase subunit B
- GenegyrB
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids796 (go to sequence)
- Protein existenceInferred from homology
- Annotation score3/5
Function
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.
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.
Catalytic activity
Cofactor
Mn2+ (UniProtKB | Rhea| CHEBI:29035 )
Ca2+ (UniProtKB | Rhea| CHEBI:29108 )
Note: Binds two Mg2+ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ or Ca2+.
Features
Showing features for binding site, site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 427 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Site | 452 | Interaction with DNA | ||||
Sequence: K | ||||||
Site | 455 | Interaction with DNA | ||||
Sequence: N | ||||||
Binding site | 501 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 501 | Mg2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 503 | Mg2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: D |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | chromosome | |
Cellular Component | cytoplasm | |
Molecular Function | ATP binding | |
Molecular Function | DNA binding | |
Molecular Function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity | |
Molecular Function | metal ion binding | |
Biological Process | DNA topological change | |
Biological Process | DNA-templated DNA replication |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA gyrase subunit B
- EC number
Gene names
Organism names
- Strain
- Taxonomic lineageBacteria > Pseudomonadota > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria
Accessions
- Primary accessionQ5F5Z6
Proteomes
Subcellular Location
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000457996 | 1-796 | DNA gyrase subunit B | |||
Sequence: MTEQKHEEYGADSIQVLEGLEAVRKRPGMYIGDTQDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDGKHESFALSGGVAGFVQYMNRKKTPLHEKIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGVMDGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDQWLLGLALEKAKIVSDGRTIEGAELADTAKQFLLAKTVIEQESRFVDELVLRAMLHASPIDLTSSENADKAVAELSGLLDEKEAALERIEGHEGHRFIKITRKLHGNVMVSYIEPKFLNSKAYQTLTQTAAALKGLVGEGAKLYKGENEYDADSFETALDILMSVAQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNIDA |
Interaction
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.
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 421-536 | Toprim | ||||
Sequence: SELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPP |
Sequence similarities
Belongs to the type II topoisomerase GyrB family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length796
- Mass (Da)88,209
- Last updated2005-03-15 v1
- ChecksumA39E518CACB144E3
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AE004969 EMBL· GenBank· DDBJ | AAW90391.1 EMBL· GenBank· DDBJ | Genomic DNA |