UniProtKB - Q5SHZ4 (GYRB_THET8)
DNA gyrase subunit B
gyrB
Functioni
Miscellaneous
Catalytic activityi
- ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation EC:5.6.2.2
Cofactori
Temperature dependencei
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 422 | Magnesium 1; catalyticUniRule annotation | 1 | |
Metal bindingi | 499 | Magnesium 1; catalyticUniRule annotation | 1 | |
Metal bindingi | 499 | Magnesium 2UniRule annotation | 1 | |
Metal bindingi | 501 | Magnesium 2UniRule annotation | 1 |
GO - Molecular functioni
- ATP binding Source: UniProtKB-UniRule
- DNA binding Source: UniProtKB-KW
- DNA negative supercoiling activity Source: UniProtKB
- metal ion binding Source: UniProtKB-KW
GO - Biological processi
- DNA-dependent DNA replication Source: UniProtKB-UniRule
- DNA topological change Source: UniProtKB-UniRule
Keywordsi
Molecular function | DNA-binding, Isomerase, Topoisomerase |
Ligand | ATP-binding, Magnesium, Metal-binding, Nucleotide-binding |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:gyrBUniRule annotation Ordered Locus Names:TTHA1586 |
Organismi | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) |
Taxonomic identifieri | 300852 [NCBI] |
Taxonomic lineagei | Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus › |
Proteomesi |
|
Subcellular locationi
- Cytoplasm UniRule annotation
GO - Cellular componenti
- chromosome Source: InterPro
- cytoplasm Source: UniProtKB-SubCell
Keywords - Cellular componenti
CytoplasmPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000435543 | 1 – 634 | DNA gyrase subunit BAdd BLAST | 634 |
Proteomic databases
PRIDEi | Q5SHZ4 |
Interactioni
Subunit structurei
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.
1 Publication1 PublicationSites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 447 | Interaction with DNAUniRule annotation | 1 | |
Sitei | 450 | Interaction with DNAUniRule annotation | 1 |
Protein-protein interaction databases
STRINGi | 300852.55772968 |
Structurei
Secondary structure
3D structure databases
SMRi | Q5SHZ4 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 416 – 534 | ToprimUniRule annotationAdd BLAST | 119 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 1 – 220 | ATPase domain1 PublicationAdd BLAST | 220 | |
Regioni | 221 – 390 | Transducer domain1 PublicationAdd BLAST | 170 |
Domaini
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG0187, Bacteria |
HOGENOMi | CLU_006146_4_1_0 |
OMAi | LWETTMH |
PhylomeDBi | Q5SHZ4 |
Family and domain databases
CDDi | cd03366, TOPRIM_TopoIIA_GyrB, 1 hit |
Gene3Di | 3.30.230.10, 1 hit 3.30.565.10, 1 hit 3.40.50.670, 1 hit |
HAMAPi | MF_01898, GyrB, 1 hit |
InterProi | View protein in InterPro IPR002288, DNA_gyrase_B_C IPR011557, GyrB IPR003594, HATPase_C IPR036890, HATPase_C_sf IPR020568, Ribosomal_S5_D2-typ_fold IPR014721, Ribosomal_S5_D2-typ_fold_subgr IPR001241, Topo_IIA IPR013760, Topo_IIA-like_dom_sf IPR013759, Topo_IIA_B_C IPR013506, Topo_IIA_bsu_dom2 IPR018522, TopoIIA_CS IPR006171, TOPRIM_domain IPR034160, TOPRIM_GyrB |
Pfami | View protein in Pfam PF00204, DNA_gyraseB, 1 hit PF00986, DNA_gyraseB_C, 1 hit PF02518, HATPase_c, 1 hit PF01751, Toprim, 1 hit |
SMARTi | View protein in SMART SM00387, HATPase_c, 1 hit SM00433, TOP2c, 1 hit |
SUPFAMi | SSF54211, SSF54211, 1 hit SSF55874, SSF55874, 1 hit SSF56719, SSF56719, 1 hit |
TIGRFAMsi | TIGR01059, gyrB, 1 hit |
PROSITEi | View protein in PROSITE PS00177, TOPOISOMERASE_II, 1 hit PS50880, TOPRIM, 1 hit |
i Sequence
Sequence statusi: Complete.
10 20 30 40 50
MSYDASAIRV LKGLEGVRHR PAMYIGGTGV EGYHHLFKEI LDNAVDEALA
60 70 80 90 100
GYATEILVRL NEDGSLTVED NGRGIPVDLM PEEGKPAVEV IYTTLHSGGK
110 120 130 140 150
FEQGAYKVSG GLHGVGASVV NALSEWTVVE VFREGKHHRI AFSRGEVTEP
160 170 180 190 200
LRVVGEAPRG KTGTRVTFKP DPEIFGNLRF DPSKIRARLR EVAYLVAGLK
210 220 230 240 250
LVFQDRQHGK EEVFLDKGGV ASFAKALAEG EDLLYEKPFL IRGTHGEVEV
260 270 280 290 300
EVGFLHTQGY NAEILTYANM IPTRDGGTHL TAFKSAYSRA LNQYAKKAGL
310 320 330 340 350
NKEKGPQPTG DDLLEGLYAV VSVKLPNPQF EGQTKGKLLN PEAGTAVGQV
360 370 380 390 400
VYERLLEILE ENPRIAKAVY EKALRAAQAR EAARKARELV RRQNPLESDE
410 420 430 440 450
LPGKLADCQT ENPEEAELFI VEGDSAGGSA KQGRDRRFQA ILPLRGKILN
460 470 480 490 500
VEKAGLSKAL KNAEVRAMVS AIGVGIGGDG EAHFDLEGLR YHKIIIMTDA
510 520 530 540 550
DVDGSHIRTL LLTFFYRYMR PLIERGHVYI AQPPLYRLQV GKKVEYLYSD
560 570 580 590 600
EELQARLKEL EGKHYEVQRF KGLGEMNPEQ LWETTMNPEK RVLKRVELQD
610 620 630
ALEASELFEK LMGQEVAPRR EFIEEHARYA ELDI
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 93 | T → N in AAF89615 (Ref. 1) Curated | 1 | |
Sequence conflicti | 475 – 476 | GI → AV in AAF89615 (Ref. 1) Curated | 2 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF167433 Genomic DNA Translation: AAF89615.1 AP008226 Genomic DNA Translation: BAD71409.1 |
RefSeqi | WP_011228788.1, NC_006461.1 YP_144852.1, NC_006461.1 |
Genome annotation databases
EnsemblBacteriai | BAD71409; BAD71409; BAD71409 |
GeneIDi | 3170041 |
KEGGi | ttj:TTHA1586 |
PATRICi | fig|300852.9.peg.1556 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF167433 Genomic DNA Translation: AAF89615.1 AP008226 Genomic DNA Translation: BAD71409.1 |
RefSeqi | WP_011228788.1, NC_006461.1 YP_144852.1, NC_006461.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1KIJ | X-ray | 2.30 | A/B | 1-390 | [»] | |
6ENH | X-ray | 1.94 | A | 1-390 | [»] | |
SMRi | Q5SHZ4 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 300852.55772968 |
Chemistry databases
DrugBanki | DB01942, Formic acid |
Proteomic databases
PRIDEi | Q5SHZ4 |
Genome annotation databases
EnsemblBacteriai | BAD71409; BAD71409; BAD71409 |
GeneIDi | 3170041 |
KEGGi | ttj:TTHA1586 |
PATRICi | fig|300852.9.peg.1556 |
Phylogenomic databases
eggNOGi | COG0187, Bacteria |
HOGENOMi | CLU_006146_4_1_0 |
OMAi | LWETTMH |
PhylomeDBi | Q5SHZ4 |
Family and domain databases
CDDi | cd03366, TOPRIM_TopoIIA_GyrB, 1 hit |
Gene3Di | 3.30.230.10, 1 hit 3.30.565.10, 1 hit 3.40.50.670, 1 hit |
HAMAPi | MF_01898, GyrB, 1 hit |
InterProi | View protein in InterPro IPR002288, DNA_gyrase_B_C IPR011557, GyrB IPR003594, HATPase_C IPR036890, HATPase_C_sf IPR020568, Ribosomal_S5_D2-typ_fold IPR014721, Ribosomal_S5_D2-typ_fold_subgr IPR001241, Topo_IIA IPR013760, Topo_IIA-like_dom_sf IPR013759, Topo_IIA_B_C IPR013506, Topo_IIA_bsu_dom2 IPR018522, TopoIIA_CS IPR006171, TOPRIM_domain IPR034160, TOPRIM_GyrB |
Pfami | View protein in Pfam PF00204, DNA_gyraseB, 1 hit PF00986, DNA_gyraseB_C, 1 hit PF02518, HATPase_c, 1 hit PF01751, Toprim, 1 hit |
SMARTi | View protein in SMART SM00387, HATPase_c, 1 hit SM00433, TOP2c, 1 hit |
SUPFAMi | SSF54211, SSF54211, 1 hit SSF55874, SSF55874, 1 hit SSF56719, SSF56719, 1 hit |
TIGRFAMsi | TIGR01059, gyrB, 1 hit |
PROSITEi | View protein in PROSITE PS00177, TOPOISOMERASE_II, 1 hit PS50880, TOPRIM, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | GYRB_THET8 | |
Accessioni | Q5SHZ4Primary (citable) accession number: Q5SHZ4 Secondary accession number(s): Q9LCX5 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | February 17, 2016 |
Last sequence update: | December 21, 2004 | |
Last modified: | December 2, 2020 | |
This is version 126 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families