Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P0C559 (GYRB_MYCSM) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 40. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA gyrase subunit B

EC=5.99.1.3
Gene names
Name:gyrB
OrganismMycobacterium smegmatis
Taxonomic identifier1772 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium

Protein attributes

Sequence length675 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings. HAMAP-Rule MF_01898

Catalytic activity

ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP-Rule MF_01898

Cofactor

Magnesium. 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+ and Ca2+ By similarity.

Subunit structure

Heterotetramer, composed of two GyrA and two GyrB chains. Within the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB contributes the cofactor binding sites and catalyzes ATP hydrolysis By similarity.

Subcellular location

Cytoplasm Potential HAMAP-Rule MF_01898.

Sequence similarities

Belongs to the type II topoisomerase family.

Contains 1 Toprim domain.

Sequence caution

The sequence CAA63253.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 675674DNA gyrase subunit B HAMAP-Rule MF_01898
PRO_0000145324

Regions

Domain453 – 567115Toprim

Sites

Metal binding4591Magnesium 1; catalytic By similarity
Metal binding5321Magnesium 1; catalytic By similarity
Metal binding5321Magnesium 2 By similarity
Metal binding5341Magnesium 2 By similarity
Site4841Interaction with DNA By similarity
Site4871Interaction with DNA By similarity

Experimental info

Sequence conflict1621G → R in CAA58884. Ref.2

Secondary structure

................................ 675
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0C559 [UniParc].

Last modified July 10, 2007. Version 1.
Checksum: 68A9B7F98BE07951

FASTA67574,512
        10         20         30         40         50         60 
MAAQKNNAPK EYGADSITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV DNAVDEAMAG 

        70         80         90        100        110        120 
FATRVDVKIH ADGSVEVRDD GRGIPVEMHA TGMPTIDVVM TQLHAGGKFD GETYAVSGGL 

       130        140        150        160        170        180 
HGVGVSVVNA LSTRLEATVL RDGYEWFQYY DRSVPGKLKQ GGETKETGTT IRFWADPEIF 

       190        200        210        220        230        240 
ETTDYNFETV ARRLQEMAFL NKGLTIELTD ERVTAEEVVD DVVKDTAEAP KTADEKAAEA 

       250        260        270        280        290        300 
TGPSKVKHRV FHYPGGLVDY VKHINRTKTP IQQSIIDFDG KGPGHEVEIA MQWNAGYSES 

       310        320        330        340        350        360 
VHTFANTINT HEGGTHEEGF RAALTSVVNR YAKDKKLLKD KDPNLTGDDI REGLAAVISV 

       370        380        390        400        410        420 
KVAEPQFEGQ TKTKLGNTEV KSFVQKICNE QLQHWFEANP AEAKTVVNKA VSSAQARIAA 

       430        440        450        460        470        480 
RKARELVRRK SATDIGGLPG KLADCRSTDP SKSELYVVEG DSAGGSAKSG RDSMFQAILP 

       490        500        510        520        530        540 
LRGKIINVEK ARIDRVLKNT EVQSIITALG TGIHDEFDIS KLRYHKIVLM ADADVDGQHI 

       550        560        570        580        590        600 
STLLLTLLFR FMKPLVENGH IFLAQPPLYK LKWQRSEPEF AYSDRERDGL LEAGRAAGKK 

       610        620        630        640        650        660 
INVDDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI LMGEDVEARR 

       670 
SFITRNAKDV RFLDV 

« Hide

References

[1]"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.
[2]"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].
Strain: SN2.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X92503 Genomic DNA. Translation: CAA63253.1. Different initiation.
X84077 Genomic DNA. Translation: CAA58884.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4B6CX-ray2.20A/B9-255[»]
4BAEX-ray2.35A/B/C/D19-212[»]
A/B/C/D247-255[»]
ProteinModelPortalP0C559.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPMF_01898. GyrB.
InterProIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSPR00418. TPI2FAMILY.
SMARTSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsTIGR01059. gyrB. 1 hit.
PROSITEPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameGYRB_MYCSM
AccessionPrimary (citable) accession number: P0C559
Secondary accession number(s): P48355, Q59555
Entry history
Integrated into UniProtKB/Swiss-Prot: July 10, 2007
Last sequence update: July 10, 2007
Last modified: July 9, 2014
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references