Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to maintain chromosomes in an underwound state, while in the absence of ATP it relaxes supercoiled dsDNA (PubMed:15047530. PubMed:16876125, PubMed:19060136, PubMed:16377674, PubMed:18426901, PubMed:22844097, PubMed:19596812, PubMed:20805881). Also catalyzes the interconversion of other topological isomers of dsDNA rings, including catenanes (PubMed:16876125, PubMed:19060136, PubMed:22457352). Gyrase from M.tuberculosis has higher decatenation than supercoiling activity compared to E.coli; as M.tuberculosis only has 1 type II topoisomerase, gyrase has to fulfill the decatenation function of topoisomerase IV as well (PubMed:16876125, PubMed:22457352, PubMed:23869946). At comparable concentrations M.tuberculosis gyrase cannot introduce as many negative supercoils into DNA as the E.coli enzyme, and its ATPase activity is lower, perhaps because it does not couple DNA wrapping and ATP binding as well as E.coli (PubMed:22457352, PubMed:24015710).11 Publications
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.

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation2 Publications

Cofactori

Mg2+UniRule annotation2 Publications, Mn2+UniRule annotationNote: Mg2+ required for DNA supercoiling, DNA relaxation, DNA cleavage and DNA decatenation, Mn2+ substitutes for relaxation but not supercoiling or cleavage activity (PubMed:16876125). Ca2+ does not substitute for supercoiling activity (PubMed:22844097).2 Publications

Enzyme regulationi

DNA supercoiling inhibited by (fluoro)quinoline antibiotics such as sparfloxacin and levofloxacin, which usually act on GyrA subunit (PubMed:15047530). DNA supercoiling inhibited by the coumarin antibiotic novobiocin which acts on GyrB (PubMed:16876125). Quinolones lead to gyrase-mediated dsDNA cleavage while preventing reclosure (PubMed:15047530, PubMed:16876125, PubMed:23869946). DNA supercoiling activity inhibited by aminopyrazinamide and pyrrolamide derivatives, probably via effects on the GyrB subunit (PubMed:23268609, PubMed:24126580). DNA relaxation inhibited by ATP and its analogs (PubMed:16876125). DNA supercoiling, relaxation, decatenation and quinolone-promoted DNA cleavage are inhibited by MfpA (50% inhibition occurs at 2 µM), inhibition of gyrase activites is enhanced in a concentration-dependent manner by MfpA (PubMed:19060136).6 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei12ATP1 Publication1
Binding sitei52ATP1 Publication1
Binding sitei79ATP1 Publication1
Binding sitei83ATP; via carbonyl oxygen1 Publication1
Binding sitei114ATP1 Publication1
Binding sitei169ATP1 Publication1
Metal bindingi459Magnesium 1; catalyticUniRule annotation1
Metal bindingi532Magnesium 1; catalyticUniRule annotation1
Metal bindingi532Magnesium 2UniRule annotation1
Metal bindingi534Magnesium 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi107 – 108ATP1 Publication2
Nucleotide bindingi120 – 125ATP1 Publication6
Nucleotide bindingi370 – 372ATP1 Publication3

GO - Molecular functioni

  • ATP binding Source: MTBBASE
  • DNA binding Source: UniProtKB-HAMAP
  • DNA supercoiling activity Source: UniProtKB
  • DNA topoisomerase type II (ATP-hydrolyzing) activity Source: MTBBASE
  • magnesium ion binding Source: MTBBASE

GO - Biological processi

  • chromosome segregation Source: GO_Central
  • DNA topological change Source: GO_Central
  • DNA unwinding involved in DNA replication Source: GO_Central
  • growth Source: MTBBASE
  • response to antibiotic Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Antibiotic resistance

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMTBH37RV:G185E-4116-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation2 Publications)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:Rv0005
ORF Names:MTCY10H4.03
OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Taxonomic identifieri83332 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001584 Componenti: Chromosome

Organism-specific databases

TubercuListiRv0005.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cell wall Source: MTBBASE
  • chromosome Source: InterPro
  • cytoplasm Source: UniProtKB-SubCell
  • DNA topoisomerase complex (ATP-hydrolyzing) Source: GO_Central
  • nucleoid Source: GO_Central
  • plasma membrane Source: MTBBASE
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi157G → S: Increased resistance to aminopyrazinamides, however genome not sequenced. 1 Publication1
Mutagenesisi169S → A: Increased resistance to pyrrolamides and novobiocin, however genome not sequenced. 1 Publication1
Mutagenesisi472D → H: No supercoiling activity. 1 Publication1
Mutagenesisi482R → K: Increased susceptibility to fluoroquinolones, half supercoiling activity, no fluoroquinolone-induced DNA cleavage (makes sequence more like E.coli). 1 Publication1
Mutagenesisi499N → D: 17-fold increased resistance to fluoroquinolones, slightly increased DNA cleavage in absence of drugs. 1 Publication1
Mutagenesisi577D → A: 37% supercoiling, 54% decatenation, 126% DNA cleavage in presence of norfloxacin. 1 Publication1
Mutagenesisi577D → R: <2% supercoiling, 4% decatenation. 1 Publication1
Mutagenesisi620 – 627ELWETTMD → ALWETTMA: <3% supercoiling, 18% decatenation, 75% DNA cleavage in presence of norfloxacin. 1 Publication8
Mutagenesisi620E → A: 15% supercoiling, 19% decatenation, 143% DNA cleavage in presence of norfloxacin. 1 Publication1
Mutagenesisi620E → R: 10% supercoiling, 7% decatenation. 1 Publication1
Mutagenesisi623E → A: 18% supercoiling, 11% decatenation, 131% DNA cleavage in presence of norfloxacin. 1 Publication1
Mutagenesisi623E → R: <2% supercoiling, 2% decatenation. 1 Publication1
Mutagenesisi627D → A: 13% supercoiling, 10% decatenation, 42% DNA cleavage in presence of norfloxacin. 1 Publication1
Mutagenesisi627D → R: <2% supercoiling, 3% decatenation. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001453251 – 675DNA gyrase subunit BAdd BLAST675

Proteomic databases

PaxDbiP9WG45.

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:15047530). 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 annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei484Interaction with DNAUniRule annotation1
Sitei487Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi83332.Rv0005.

Structurei

Secondary structure

1675
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 16Combined sources3
Helixi24 – 28Combined sources5
Helixi31 – 34Combined sources4
Helixi39 – 58Combined sources20
Beta strandi64 – 69Combined sources6
Beta strandi75 – 79Combined sources5
Beta strandi92 – 94Combined sources3
Helixi95 – 101Combined sources7
Beta strandi105 – 107Combined sources3
Beta strandi109 – 113Combined sources5
Helixi124 – 130Combined sources7
Beta strandi132 – 141Combined sources10
Beta strandi144 – 151Combined sources8
Beta strandi159 – 163Combined sources5
Beta strandi168 – 175Combined sources8
Turni177 – 179Combined sources3
Helixi187 – 199Combined sources13
Beta strandi205 – 210Combined sources6
Helixi236 – 241Combined sources6
Beta strandi247 – 251Combined sources5
Turni254 – 256Combined sources3
Helixi257 – 264Combined sources8
Turni265 – 267Combined sources3
Beta strandi270 – 274Combined sources5
Beta strandi276 – 282Combined sources7
Beta strandi285 – 298Combined sources14
Beta strandi300 – 305Combined sources6
Helixi315 – 334Combined sources20
Helixi347 – 351Combined sources5
Beta strandi354 – 360Combined sources7
Turni369 – 372Combined sources4
Helixi378 – 398Combined sources21
Helixi400 – 422Combined sources23
Helixi450 – 452Combined sources3
Beta strandi453 – 462Combined sources10
Beta strandi475 – 481Combined sources7
Turni488 – 490Combined sources3
Helixi493 – 496Combined sources4
Helixi500 – 509Combined sources10
Helixi514 – 516Combined sources3
Helixi519 – 521Combined sources3
Beta strandi525 – 530Combined sources6
Helixi535 – 551Combined sources17
Helixi554 – 557Combined sources4
Beta strandi561 – 564Combined sources4
Beta strandi568 – 571Combined sources4
Beta strandi573 – 576Combined sources4
Beta strandi579 – 583Combined sources5
Helixi584 – 597Combined sources14
Turni603 – 605Combined sources3
Beta strandi606 – 609Combined sources4
Helixi613 – 615Combined sources3
Helixi618 – 625Combined sources8
Turni628 – 630Combined sources3
Beta strandi633 – 635Combined sources3
Helixi638 – 653Combined sources16
Helixi656 – 666Combined sources11
Helixi667 – 672Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ZJTX-ray2.80A/B448-675[»]
3IG0X-ray2.10A448-675[»]
3M4IX-ray1.95A448-675[»]
3ZKBX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P2-427[»]
3ZKDX-ray2.95A/B/C/D/E/F/G/H2-427[»]
3ZM7X-ray3.30A/B/C/D/E/F2-428[»]
5BS8X-ray2.40B/D426-675[»]
5BTAX-ray2.55B/D426-675[»]
5BTCX-ray2.55B/D426-675[»]
5BTDX-ray2.50B/D426-675[»]
5BTFX-ray2.61B/D426-675[»]
5BTGX-ray2.50B/D426-675[»]
5BTIX-ray2.50B/D426-675[»]
5BTLX-ray2.50B/D426-675[»]
5BTNX-ray2.50B/D426-675[»]
ProteinModelPortaliP9WG45.
SMRiP9WG45.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini453 – 567ToprimUniRule annotationAdd BLAST115

Domaini

The B' domain (residues 448-675, Toprim plus a tail domain) forms a dimer; when reconstituted with intact GyrA the complex has ATP-independent DNA relaxation activity (PubMed:19596812). The same fragment (also called TopBK) when reconstituted with intact GyrA or the N-terminus of GyrA (residues 1-502) can catalyze quinolone-mediated DNA breaks (PubMed:20805881).2 Publications

Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
KOiK02470.
OMAiIKNMITA.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P9WG45-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAQKKKAQD EYGAASITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV
60 70 80 90 100
DNAVDEAMAG YATTVNVVLL EDGGVEVADD GRGIPVATHA SGIPTVDVVM
110 120 130 140 150
TQLHAGGKFD SDAYAISGGL HGVGVSVVNA LSTRLEVEIK RDGYEWSQVY
160 170 180 190 200
EKSEPLGLKQ GAPTKKTGST VRFWADPAVF ETTEYDFETV ARRLQEMAFL
210 220 230 240 250
NKGLTINLTD ERVTQDEVVD EVVSDVAEAP KSASERAAES TAPHKVKSRT
260 270 280 290 300
FHYPGGLVDF VKHINRTKNA IHSSIVDFSG KGTGHEVEIA MQWNAGYSES
310 320 330 340 350
VHTFANTINT HEGGTHEEGF RSALTSVVNK YAKDRKLLKD KDPNLTGDDI
360 370 380 390 400
REGLAAVISV KVSEPQFEGQ TKTKLGNTEV KSFVQKVCNE QLTHWFEANP
410 420 430 440 450
TDAKVVVNKA VSSAQARIAA RKARELVRRK SATDIGGLPG KLADCRSTDP
460 470 480 490 500
RKSELYVVEG DSAGGSAKSG RDSMFQAILP LRGKIINVEK ARIDRVLKNT
510 520 530 540 550
EVQAIITALG TGIHDEFDIG KLRYHKIVLM ADADVDGQHI STLLLTLLFR
560 570 580 590 600
FMRPLIENGH VFLAQPPLYK LKWQRSDPEF AYSDRERDGL LEAGLKAGKK
610 620 630 640 650
INKEDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI
660 670
LMGEDVDARR SFITRNAKDV RFLDV
Length:675
Mass (Da):74,091
Last modified:April 16, 2014 - v1
Checksum:i4559D0D3FDAC8DC1
GO

Sequence cautioni

The sequence AAA83016 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti291 – 292MQ → IE in AAA83016 (PubMed:8031045).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27512 Genomic DNA. Translation: AAA83016.1. Different initiation.
AL123456 Genomic DNA. Translation: CCP42727.1.
PIRiS44198.
RefSeqiNP_214519.2. NC_000962.3.
WP_003917863.1. NZ_KK339370.1.

Genome annotation databases

EnsemblBacteriaiCCP42727; CCP42727; Rv0005.
GeneIDi887081.
KEGGimtu:Rv0005.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27512 Genomic DNA. Translation: AAA83016.1. Different initiation.
AL123456 Genomic DNA. Translation: CCP42727.1.
PIRiS44198.
RefSeqiNP_214519.2. NC_000962.3.
WP_003917863.1. NZ_KK339370.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ZJTX-ray2.80A/B448-675[»]
3IG0X-ray2.10A448-675[»]
3M4IX-ray1.95A448-675[»]
3ZKBX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P2-427[»]
3ZKDX-ray2.95A/B/C/D/E/F/G/H2-427[»]
3ZM7X-ray3.30A/B/C/D/E/F2-428[»]
5BS8X-ray2.40B/D426-675[»]
5BTAX-ray2.55B/D426-675[»]
5BTCX-ray2.55B/D426-675[»]
5BTDX-ray2.50B/D426-675[»]
5BTFX-ray2.61B/D426-675[»]
5BTGX-ray2.50B/D426-675[»]
5BTIX-ray2.50B/D426-675[»]
5BTLX-ray2.50B/D426-675[»]
5BTNX-ray2.50B/D426-675[»]
ProteinModelPortaliP9WG45.
SMRiP9WG45.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv0005.

Proteomic databases

PaxDbiP9WG45.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCP42727; CCP42727; Rv0005.
GeneIDi887081.
KEGGimtu:Rv0005.

Organism-specific databases

TubercuListiRv0005.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
KOiK02470.
OMAiIKNMITA.

Enzyme and pathway databases

BioCyciMTBH37RV:G185E-4116-MONOMER.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGYRB_MYCTU
AccessioniPrimary (citable) accession number: P9WG45
Secondary accession number(s): L0T585
, P0C5C5, P41514, P77897
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: November 2, 2016
This is version 25 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

When the enzyme transiently cleaves DNA a phosphotyrosine bond is formed between GyrA and DNA (PubMed:15047530). In the presence of quinolones this intermediate can be trapped and is used as an indicator of drug toxicity (PubMed:16377674, PubMed:16876125, PubMed:23869946). DNA gyrase is intrinsically more resistant to fluoroquinolone drugs than in E.coli, mutating it to resemble E.coli increases its susceptibility to fluoroquinolones (most quinolone-resistant mutations are in the GyrA subunit) (PubMed:18426901).4 Publications1 Publication
Gyrase from M.tuberculosis is usually assayed in the presence of potassium glutamate (KGlu); KGlu stimulates supercoiling but inhibits DNA relaxation activity, and has concentration-dependent effects on GyrA-box mutants (PubMed:16876125, PubMed:23869946).2 Publications
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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.