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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
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 (PubMed:8878580) 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 annotation1 Publication

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ca2+UniRule annotationNote: 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+.UniRule annotation

Enzyme regulationi

Inhibited by 4-quinoline drugs (nalidixic acid, ciprofloxacin, ofloxacin), although it is much less sensitive than the corresponding enzyme from E.coli (PubMed:8878580). GyrB intrinsic ATPase activity inhibited by aminopyrazinamide and pyrrolamide derivatives (PubMed:23268609, PubMed:24126580).3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi459 – 4591Magnesium 1; catalyticUniRule annotation
Metal bindingi532 – 5321Magnesium 1; catalyticUniRule annotation
Metal bindingi532 – 5321Magnesium 2UniRule annotation
Metal bindingi534 – 5341Magnesium 2UniRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • DNA binding Source: UniProtKB-HAMAP
  • DNA supercoiling activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciMSME246196:GJ4Y-5-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:MSMEG_0005, MSMEI_0007
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
Proteomesi
  • UP000006158 Componenti: Chromosome
  • UP000000757 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL6059.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 675674DNA gyrase subunit BPRO_0000293599Add
BLAST

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:8878580). 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

STRINGi246196.MSMEG_0005.

Structurei

Secondary structure

1
675
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi24 – 285Combined sources
Helixi31 – 344Combined sources
Helixi39 – 5820Combined sources
Beta strandi64 – 696Combined sources
Beta strandi73 – 797Combined sources
Beta strandi90 – 945Combined sources
Helixi95 – 1017Combined sources
Helixi127 – 1304Combined sources
Beta strandi131 – 14111Combined sources
Beta strandi144 – 1518Combined sources
Beta strandi159 – 1635Combined sources
Beta strandi168 – 1758Combined sources
Turni177 – 1793Combined sources
Helixi187 – 20014Combined sources
Beta strandi205 – 2106Combined sources
Turni211 – 2133Combined sources
Beta strandi248 – 2514Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4B6CX-ray2.20A/B9-255[»]
4BAEX-ray2.35A/B/C/D19-212[»]
A/B/C/D247-255[»]
ProteinModelPortaliA0QNE0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075154.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.

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.
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.

Sequence processingi: The displayed sequence is further processed into a mature form.

A0QNE0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAQKNNAPK EYGADSITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV
60 70 80 90 100
DNAVDEAMAG FATRVDVKIH ADGSVEVRDD GRGIPVEMHA TGMPTIDVVM
110 120 130 140 150
TQLHAGGKFD GETYAVSGGL HGVGVSVVNA LSTRLEATVL RDGYEWFQYY
160 170 180 190 200
DRSVPGKLKQ GGETKETGTT IRFWADPEIF ETTDYNFETV ARRLQEMAFL
210 220 230 240 250
NKGLTIELTD ERVTAEEVVD DVVKDTAEAP KTADEKAAEA TGPSKVKHRV
260 270 280 290 300
FHYPGGLVDY VKHINRTKTP IQQSIIDFDG KGPGHEVEIA MQWNAGYSES
310 320 330 340 350
VHTFANTINT HEGGTHEEGF RAALTSVVNR YAKDKKLLKD KDPNLTGDDI
360 370 380 390 400
REGLAAVISV KVAEPQFEGQ TKTKLGNTEV KSFVQKICNE QLQHWFEANP
410 420 430 440 450
AEAKTVVNKA VSSAQARIAA RKARELVRRK SATDIGGLPG KLADCRSTDP
460 470 480 490 500
SKSELYVVEG DSAGGSAKSG RDSMFQAILP LRGKIINVEK ARIDRVLKNT
510 520 530 540 550
EVQSIITALG TGIHDEFDIS KLRYHKIVLM ADADVDGQHI STLLLTLLFR
560 570 580 590 600
FMKPLVENGH IFLAQPPLYK LKWQRSEPEF AYSDRERDGL LEAGRAAGKK
610 620 630 640 650
INVDDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI
660 670
LMGEDVEARR SFITRNAKDV RFLDV
Length:675
Mass (Da):74,512
Last modified:January 9, 2007 - v1
Checksum:i68A9B7F98BE07951
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti442 – 4421L → S in CAA63917 (PubMed:8878580).Curated
Sequence conflicti507 – 5071T → R in CAA63917 (PubMed:8878580).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X94224 Genomic DNA. Translation: CAA63917.1.
CP000480 Genomic DNA. Translation: ABK72750.1.
CP001663 Genomic DNA. Translation: AFP36492.1.
RefSeqiWP_003891333.1. NZ_CP009494.1.
YP_884428.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK72750; ABK72750; MSMEG_0005.
AFP36492; AFP36492; MSMEI_0007.
GeneIDi4531510.
KEGGimsb:LJ00_00025.
msg:MSMEI_0007.
msm:MSMEG_0005.
PATRICi18072478. VBIMycSme59918_0005.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X94224 Genomic DNA. Translation: CAA63917.1.
CP000480 Genomic DNA. Translation: ABK72750.1.
CP001663 Genomic DNA. Translation: AFP36492.1.
RefSeqiWP_003891333.1. NZ_CP009494.1.
YP_884428.1. NC_008596.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4B6CX-ray2.20A/B9-255[»]
4BAEX-ray2.35A/B/C/D19-212[»]
A/B/C/D247-255[»]
ProteinModelPortaliA0QNE0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_0005.

Chemistry

ChEMBLiCHEMBL6059.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK72750; ABK72750; MSMEG_0005.
AFP36492; AFP36492; MSMEI_0007.
GeneIDi4531510.
KEGGimsb:LJ00_00025.
msg:MSMEI_0007.
msm:MSMEG_0005.
PATRICi18072478. VBIMycSme59918_0005.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075154.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.

Enzyme and pathway databases

BioCyciMSME246196:GJ4Y-5-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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence analysis, purification, and study of inhibition by 4-quinolones of the DNA gyrase from Mycobacterium smegmatis."
    Revel-Viravau V., Truong Q.C., Moreau N., Jarlier V., Sougakoff W.
    Antimicrob. Agents Chemother. 40:2054-2061(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-12, FUNCTION, SUBUNIT, ENZYME REGULATION.
    Strain: ATCC 700084 / mc(2)155.
  2. Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C., Fraser C.M.
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  3. "Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
    Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
    Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  4. "Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
    Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
    Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  5. "Aminopyrazinamides: novel and specific GyrB inhibitors that kill replicating and nonreplicating Mycobacterium tuberculosis."
    Shirude P.S., Madhavapeddi P., Tucker J.A., Murugan K., Patil V., Basavarajappa H., Raichurkar A.V., Humnabadkar V., Hussein S., Sharma S., Ramya V.K., Narayan C.B., Balganesh T.S., Sambandamurthy V.K.
    ACS Chem. Biol. 8:519-523(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 9-255 IN COMPLEX WITH AMINOPYRAZINAMIDE, ENZYME REGULATION.
  6. Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 19-212 AND 247-255 IN COMPLEX WITH PYRROLAMIDE, ENZYME REGULATION.

Entry informationi

Entry nameiGYRB_MYCS2
AccessioniPrimary (citable) accession number: A0QNE0
Secondary accession number(s): I7FVC1, P48355, Q59555
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 10, 2007
Last sequence update: January 9, 2007
Last modified: June 8, 2016
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.