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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Mycobacterium smegmatis
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Supercoils relaxed DNA in an ATP-dependent manner (PubMed:8574396). 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, also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:12000834). At comparable concentrations has a stronger decatenation activity than E.coli, which is inhibited by ciprofloxacin and novobiocin (PubMed:12000834). Cleaves dsDNA at the sequence 5'-AT/GGCC-3', leaving a 4 base overhang (PubMed:12000834). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:12000834).2 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 annotation1 Publication

Cofactori

Mg2+UniRule annotation1 Publication, 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

DNA supercoiling is inhibited by the coumarin antibiotic novobiocin (PubMed:8574396). Also inhibited by the fluoroquinolones ciprofloxacin and moxifloxacin (PubMed:12000834).2 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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
OrganismiMycobacterium smegmatis
Taxonomic identifieri1772 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL3085613.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 675674DNA gyrase subunit BPRO_0000145324Add
BLAST

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:12000834, PubMed:8574396). 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 Publication1 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.

Chemistry

BindingDBiP0C559.

Structurei

3D structure databases

ProteinModelPortaliP0C559.
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.
KOiK02470.

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.

P0C559-1 [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:July 10, 2007 - v1
Checksum:i68A9B7F98BE07951
GO

Sequence cautioni

The sequence CAA63253.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti162 – 1621G → R in CAA58884 (PubMed:8574396).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X92503 Genomic DNA. Translation: CAA63253.1. Different initiation.
X84077 Genomic DNA. Translation: CAA58884.1.
RefSeqiWP_003891333.1. NZ_CP009496.1.

Genome annotation databases

KEGGimsh:LI98_00025.
msn:LI99_00025.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X92503 Genomic DNA. Translation: CAA63253.1. Different initiation.
X84077 Genomic DNA. Translation: CAA58884.1.
RefSeqiWP_003891333.1. NZ_CP009496.1.

3D structure databases

ProteinModelPortaliP0C559.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_0005.

Chemistry

BindingDBiP0C559.
ChEMBLiCHEMBL3085613.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGimsh:LI98_00025.
msn:LI99_00025.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
KOiK02470.

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

  1. "Mycobacterium smegmatis DNA gyrase: cloning and overexpression in Escherichia coli."
    Madhusudan K., Nagaraja V.
    Microbiology 141:3029-3037(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, ENZYME REGULATION, SUBUNIT.
    Strain: ATCC 27204 / DSM 43464 / SN2.
  2. "Organization of the origins of replication of the chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium tuberculosis and isolation of a functional origin from M. smegmatis."
    Salazar L., Fsihi H., De Rossi E., Riccardi G., Rios C., Cole S.T., Takiff H.E.
    Mol. Microbiol. 20:283-293(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692.
  3. "Functional characterisation of mycobacterial DNA gyrase: an efficient decatenase."
    Manjunatha U.H., Dalal M., Chatterji M., Radha D.R., Visweswariah S.S., Nagaraja V.
    Nucleic Acids Res. 30:2144-2153(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, SUBUNIT, SUBCELLULAR LOCATION, DNA-BINDING.
    Strain: ATCC 27204 / DSM 43464 / SN2.

Entry informationi

Entry nameiGYRB_MYCSM
AccessioniPrimary (citable) accession number: P0C559
Secondary accession number(s): P48355, Q59555
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 10, 2007
Last sequence update: July 10, 2007
Last modified: March 16, 2016
This is version 49 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

Documents

  1. 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.