Q5SHZ4 · GYRB_THET8
- ProteinDNA gyrase subunit B
- GenegyrB
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids634 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner (PubMed:11850422, PubMed:23804759).
It probably also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:11850422).
Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:11850422, PubMed:23804759).
At comparable concentrations T.thermophilus gyrase does not introduce as many negative supercoils into DNA as the E.coli enzyme (PubMed:23804759).
It probably also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:11850422).
Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:11850422, PubMed:23804759).
At comparable concentrations T.thermophilus gyrase does not introduce as many negative supercoils into DNA as the E.coli enzyme (PubMed:23804759).
Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.
Miscellaneous
For the electron microscopy studies a GyrB-GyrA fusion protein was made with a Gly-Asp-Leu linker between the 2 subunits. It forms the expected dimer (PubMed:23804759).
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+.
Temperature Dependence
Optimum temperature is 65 degrees Celsius (PubMed:11850422, PubMed:23804759).
Active between 25 and 77 degrees Celsius (PubMed:11850422).
Active between 25 and 77 degrees Celsius (PubMed:11850422).
Features
Showing features for binding site, site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 422 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Site | 447 | Interaction with DNA | ||||
Sequence: K | ||||||
Site | 450 | Interaction with DNA | ||||
Sequence: N | ||||||
Binding site | 499 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 499 | Mg2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 501 | 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 negative supercoiling 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 > Deinococcota > Deinococci > Thermales > Thermaceae > Thermus
Accessions
- Primary accessionQ5SHZ4
- Secondary accessions
Proteomes
Subcellular Location
Phenotypes & Variants
Chemistry
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000435543 | 1-634 | DNA gyrase subunit B | |||
Sequence: MSYDASAIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYTTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKARELVRRQNPLESDELPGKLADCQTENPEEAELFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKAGLSKALKNAEVRAMVSAIGVGIGGDGEAHFDLEGLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIERGHVYIAQPPLYRLQVGKKVEYLYSDEELQARLKELEGKHYEVQRFKGLGEMNPEQLWETTMNPEKRVLKRVELQDALEASELFEKLMGQEVAPRREFIEEHARYAELDI |
Interaction
Subunit
Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:23804759).
Non-hydrolyzable ATP analogs induce dimerization, novobiocin also induces a small amount of dimerization (PubMed:11850422).
The two subunits form an intertwined dimer where the GyrB ATPase transducer helix of 1 subunit connects to the Toprim domain of the other GyrB subunit through a 10 residue linker (PubMed:23804759).
In the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis
Non-hydrolyzable ATP analogs induce dimerization, novobiocin also induces a small amount of dimerization (PubMed:11850422).
The two subunits form an intertwined dimer where the GyrB ATPase transducer helix of 1 subunit connects to the Toprim domain of the other GyrB subunit through a 10 residue linker (PubMed:23804759).
In the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis
Structure
Family & Domains
Features
Showing features for region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-220 | ATPase domain | ||||
Sequence: MSYDASAIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYTTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGV | ||||||
Region | 221-390 | Transducer domain | ||||
Sequence: ASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKARELV | ||||||
Domain | 416-534 | Toprim | ||||
Sequence: AELFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKAGLSKALKNAEVRAMVSAIGVGIGGDGEAHFDLEGLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIERGHVYIAQPP |
Domain
Consists of 3 domains; the ATPase domain (residues 1-220), the transducer domain (221-390) and the toprim domain (391-634) (PubMed:11850422).
Removal of the N-terminal ATPase domain (residues 2-392) increases ATP-independent DNA relaxation, showing it is not required for DNA binding or cleavage, this enzyme still has some supercoiling activity, but in this case it introduces positive supercoils (PubMed:23804759).
Removal of the N-terminal ATPase domain (residues 2-392) increases ATP-independent DNA relaxation, showing it is not required for DNA binding or cleavage, this enzyme still has some supercoiling activity, but in this case it introduces positive supercoils (PubMed:23804759).
Sequence similarities
Belongs to the type II topoisomerase GyrB family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length634
- Mass (Da)70,524
- Last updated2004-12-21 v1
- Checksum1276B82F82DAC561
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 93 | in Ref. 1; AAF89615 | ||||
Sequence: T → N | ||||||
Sequence conflict | 475-476 | in Ref. 1; AAF89615 | ||||
Sequence: GI → AV |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AF167433 EMBL· GenBank· DDBJ | AAF89615.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AP008226 EMBL· GenBank· DDBJ | BAD71409.1 EMBL· GenBank· DDBJ | Genomic DNA |