UniProtKB - A4XN63 (A4XN63_PSEMY)
Protein
DNA gyrase subunit B
Gene
gyrB
Organism
Pseudomonas mendocina (strain ymp)
Status
Functioni
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.UniRule annotationARBA annotation
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.UniRule annotation
Catalytic activityi
- ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotationARBA annotation EC:5.6.2.2
Cofactori
Mg2+ARBA annotation
GO - Molecular functioni
- ATP binding Source: UniProtKB-UniRule
- DNA binding Source: InterPro
- DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity Source: UniProtKB-UniRule
- 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-bindingARBA annotation, Isomerase, TopoisomeraseUniRule annotationARBA annotation |
Ligand | ATP-bindingUniRule annotationARBA annotation, MagnesiumARBA annotation, Metal-bindingARBA annotation, Nucleotide-binding |
Enzyme and pathway databases
BioCyci | PMEN399739:PMEN_RS00020-MONOMER |
Names & Taxonomyi
Protein namesi | Recommended name: DNA gyrase subunit BUniRule annotationARBA annotation (EC:5.6.2.2UniRule annotationARBA annotation) |
Gene namesi | Name:gyrBUniRule annotation Ordered Locus Names:Pmen_0004Imported |
Organismi | Pseudomonas mendocina (strain ymp)Imported |
Taxonomic identifieri | 399739 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › |
Proteomesi |
|
Subcellular locationi
- Cytoplasm UniRule annotation
GO - Cellular componenti
- chromosome Source: InterPro
- cytoplasm Source: UniProtKB-SubCell
Keywords - Cellular componenti
CytoplasmUniRule annotationInteractioni
Subunit structurei
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.
UniRule annotationARBA annotationProtein-protein interaction databases
STRINGi | 399739.Pmen_0004 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 420 – 535 | ToprimInterPro annotationAdd BLAST | 116 |
Sequence similaritiesi
Belongs to the type II topoisomerase GyrB family.ARBA annotation
Belongs to the type II topoisomerase family.UniRule annotation
Phylogenomic databases
eggNOGi | COG0187, Bacteria |
HOGENOMi | CLU_006146_4_1_6 |
OMAi | LWETTMH |
OrthoDBi | 205481at2 |
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, 2 hits |
HAMAPi | MF_01898, GyrB, 1 hit |
InterProi | View protein in InterPro IPR002288, DNA_gyrase_B_C IPR011557, GyrB IPR041423, GyrB_insert 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 PF18053, GyrB_insert, 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.
A4XN63-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MSENQTYDSS SIKVLKGLDA VRKRPGMYIG DTDDGSGLHH MVFEVVDNSI
60 70 80 90 100
DEALAGYCSE IVITIHPDES ISVRDNGRGI PVDIHKEEGV SAAEVIMTVL
110 120 130 140 150
HAGGKFDDNT YKVSGGLHGV GVSVVNALSE ELRLTIRRAG KVWEQIYHHG
160 170 180 190 200
VPQAPLATVG DTDGTGTEIH FKASAETFSN IHFSWDILAK RLRELSFLNS
210 220 230 240 250
GVGILLRDER SGKEELFKYE GGLKAFVEYL NTNKNVVNQV FHFNIQREED
260 270 280 290 300
GVGVEVALQW NDSFNENILC FTNNIPQRDG GTHLAGFRSA LTRHLNNYIE
310 320 330 340 350
QEGLAKKFKV ATTGDDAREG LTAIISVKVP DPKFSSQTKD KLVSSEVKTA
360 370 380 390 400
VEQEMGKYFA DFLLENPNEA KAVVGKMIDA ARAREAARKA REMTRRKGAL
410 420 430 440 450
DIAGLPGKLA DCQEKDPALS ELYIVEGDSA GGSAKQGRNR KTQAILPLKG
460 470 480 490 500
KILNVEKARF DKMLSSAEVG TLITALGCGI GREEYNIDKL RYHNIIIMTD
510 520 530 540 550
ADVDGSHIRT LLLTFFFRQL PELIERGYVY IAQPPLYKVK KGKQEQYIKD
560 570 580 590 600
DEAMDEYMTQ SALEDASLHV NENAPGLSGG ALEKLVGEYR GVMKTLDRLS
610 620 630 640 650
RVYPKEITEH FVYLPRIGLE QLADHAGMQA WLEQFSARLK TMEKSGQTYT
660 670 680 690 700
ASLREDRERH VWLPEVEVKA HGLSSYTTFN RDFFASNDYK TVTALGDQLN
710 720 730 740 750
NLLEDSAYVQ RGERKKPVAT FKEALDWLMA ESTKRHSIQR YKGLGEMNPD
760 770 780 790 800
QLWETTMDPE VRRMLKVTIE DAIAADQIFN TLMGDAVEPR RDFIESNALA
VSNLDF
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | CP000680 Genomic DNA Translation: ABP82779.1 |
RefSeqi | WP_003246706.1, NC_009439.1 |
Genome annotation databases
EnsemblBacteriai | ABP82779; ABP82779; Pmen_0004 |
GeneIDi | 5106679 |
KEGGi | pmy:Pmen_0004 |
PATRICi | fig|399739.8.peg.5 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | CP000680 Genomic DNA Translation: ABP82779.1 |
RefSeqi | WP_003246706.1, NC_009439.1 |
3D structure databases
ModBasei | Search... |
SWISS-MODEL-Workspacei | Submit a new modelling project... |
Protein-protein interaction databases
STRINGi | 399739.Pmen_0004 |
Genome annotation databases
EnsemblBacteriai | ABP82779; ABP82779; Pmen_0004 |
GeneIDi | 5106679 |
KEGGi | pmy:Pmen_0004 |
PATRICi | fig|399739.8.peg.5 |
Phylogenomic databases
eggNOGi | COG0187, Bacteria |
HOGENOMi | CLU_006146_4_1_6 |
OMAi | LWETTMH |
OrthoDBi | 205481at2 |
Enzyme and pathway databases
BioCyci | PMEN399739:PMEN_RS00020-MONOMER |
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, 2 hits |
HAMAPi | MF_01898, GyrB, 1 hit |
InterProi | View protein in InterPro IPR002288, DNA_gyrase_B_C IPR011557, GyrB IPR041423, GyrB_insert 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 PF18053, GyrB_insert, 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 | A4XN63_PSEMY | |
Accessioni | A4XN63Primary (citable) accession number: A4XN63 | |
Entry historyi | Integrated into UniProtKB/TrEMBL: | May 29, 2007 |
Last sequence update: | May 29, 2007 | |
Last modified: | December 2, 2020 | |
This is version 103 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Unreviewed (UniProtKB/TrEMBL) |