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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121ATP1 Publication
Binding sitei52 – 521ATP1 Publication
Binding sitei79 – 791ATP1 Publication
Binding sitei83 – 831ATP; via carbonyl oxygen1 Publication
Binding sitei114 – 1141ATP1 Publication
Binding sitei169 – 1691ATP1 Publication
Metal bindingi459 – 4591Magnesium 1; catalyticUniRule annotation
Metal bindingi532 – 5321Magnesium 1; catalyticUniRule annotation
Metal bindingi532 – 5321Magnesium 2UniRule annotation
Metal bindingi534 – 5341Magnesium 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi107 – 1082ATP1 Publication
Nucleotide bindingi120 – 1256ATP1 Publication
Nucleotide bindingi370 – 3723ATP1 Publication

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

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi157 – 1571G → S: Increased resistance to aminopyrazinamides, however genome not sequenced. 1 Publication
Mutagenesisi169 – 1691S → A: Increased resistance to pyrrolamides and novobiocin, however genome not sequenced. 1 Publication
Mutagenesisi472 – 4721D → H: No supercoiling activity. 1 Publication
Mutagenesisi482 – 4821R → K: Increased susceptibility to fluoroquinolones, half supercoiling activity, no fluoroquinolone-induced DNA cleavage (makes sequence more like E.coli). 1 Publication
Mutagenesisi499 – 4991N → D: 17-fold increased resistance to fluoroquinolones, slightly increased DNA cleavage in absence of drugs. 1 Publication
Mutagenesisi577 – 5771D → A: 37% supercoiling, 54% decatenation, 126% DNA cleavage in presence of norfloxacin. 1 Publication
Mutagenesisi577 – 5771D → R: <2% supercoiling, 4% decatenation. 1 Publication
Mutagenesisi620 – 6278ELWETTMD → ALWETTMA: <3% supercoiling, 18% decatenation, 75% DNA cleavage in presence of norfloxacin. 1 Publication
Mutagenesisi620 – 6201E → A: 15% supercoiling, 19% decatenation, 143% DNA cleavage in presence of norfloxacin. 1 Publication
Mutagenesisi620 – 6201E → R: 10% supercoiling, 7% decatenation. 1 Publication
Mutagenesisi623 – 6231E → A: 18% supercoiling, 11% decatenation, 131% DNA cleavage in presence of norfloxacin. 1 Publication
Mutagenesisi623 – 6231E → R: <2% supercoiling, 2% decatenation. 1 Publication
Mutagenesisi627 – 6271D → A: 13% supercoiling, 10% decatenation, 42% DNA cleavage in presence of norfloxacin. 1 Publication
Mutagenesisi627 – 6271D → R: <2% supercoiling, 3% decatenation. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 675675DNA gyrase subunit BPRO_0000145325Add
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Sitei484 – 4841Interaction with DNAUniRule annotation
Sitei487 – 4871Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi83332.Rv0005.

Structurei

Secondary structure

1
675
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi14 – 163Combined sources
Helixi24 – 285Combined sources
Helixi31 – 344Combined sources
Helixi39 – 5820Combined sources
Beta strandi64 – 696Combined sources
Beta strandi75 – 795Combined sources
Beta strandi92 – 943Combined sources
Helixi95 – 1017Combined sources
Beta strandi105 – 1073Combined sources
Beta strandi109 – 1135Combined sources
Helixi124 – 1307Combined sources
Beta strandi132 – 14110Combined sources
Beta strandi144 – 1518Combined sources
Beta strandi159 – 1635Combined sources
Beta strandi168 – 1758Combined sources
Turni177 – 1793Combined sources
Helixi187 – 19913Combined sources
Beta strandi205 – 2106Combined sources
Helixi236 – 2416Combined sources
Beta strandi247 – 2515Combined sources
Turni254 – 2563Combined sources
Helixi257 – 2648Combined sources
Turni265 – 2673Combined sources
Beta strandi270 – 2745Combined sources
Beta strandi276 – 2827Combined sources
Beta strandi285 – 29814Combined sources
Beta strandi300 – 3056Combined sources
Helixi315 – 33420Combined sources
Helixi347 – 3515Combined sources
Beta strandi354 – 3607Combined sources
Turni369 – 3724Combined sources
Helixi378 – 39821Combined sources
Helixi400 – 42223Combined sources
Helixi450 – 4523Combined sources
Beta strandi453 – 46210Combined sources
Beta strandi475 – 4817Combined sources
Turni488 – 4903Combined sources
Helixi493 – 4964Combined sources
Helixi500 – 50910Combined sources
Helixi514 – 5163Combined sources
Helixi519 – 5213Combined sources
Beta strandi525 – 5306Combined sources
Helixi535 – 55117Combined sources
Helixi554 – 5574Combined sources
Beta strandi561 – 5644Combined sources
Beta strandi568 – 5714Combined sources
Beta strandi573 – 5764Combined sources
Beta strandi579 – 5835Combined sources
Helixi584 – 59714Combined sources
Turni603 – 6053Combined sources
Beta strandi606 – 6094Combined sources
Helixi613 – 6153Combined sources
Helixi618 – 6258Combined sources
Turni628 – 6303Combined sources
Beta strandi633 – 6353Combined sources
Helixi638 – 65316Combined sources
Helixi656 – 66611Combined sources
Helixi667 – 6726Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 12-421, 448-654.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini453 – 567115ToprimUniRule annotationAdd
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti291 – 2922MQ → IE in AAA83016 (PubMed:8031045).Curated

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
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. Positions 12-421, 448-654.
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.

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: June 8, 2016
This is version 23 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.