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P0C559

- GYRB_MYCSM

UniProt

P0C559 - GYRB_MYCSM

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Protein
DNA gyrase subunit B
Gene
gyrB
Organism
Mycobacterium smegmatis
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

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

Cofactori

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi459 – 4591Magnesium 1; catalytic By similarity
Sitei484 – 4841Interaction with DNA By similarity
Sitei487 – 4871Interaction with DNA By similarity
Metal bindingi532 – 5321Magnesium 1; catalytic By similarity
Metal bindingi532 – 5321Magnesium 2 By similarity
Metal bindingi534 – 5341Magnesium 2 By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA topological change Source: InterPro
  2. DNA-dependent DNA replication Source: UniProtKB-HAMAP
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 B (EC:5.99.1.3)
Gene namesi
Name:gyrB
OrganismiMycobacterium smegmatis
Taxonomic identifieri1772 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium

Subcellular locationi

Cytoplasm Reviewed prediction UniRule annotation

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed By similarity
Chaini2 – 675674DNA gyrase subunit BUniRule annotation
PRO_0000145324Add
BLAST

Interactioni

Subunit structurei

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.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4B6CX-ray2.20A/B9-255[»]
4BAEX-ray2.35A/B/C/D19-212[»]
A/B/C/D247-255[»]
ProteinModelPortaliP0C559.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini453 – 567115Toprim
Add
BLAST

Sequence similaritiesi

Contains 1 Toprim domain.

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_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]
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

MAAQKNNAPK EYGADSITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV    50
DNAVDEAMAG FATRVDVKIH ADGSVEVRDD GRGIPVEMHA TGMPTIDVVM 100
TQLHAGGKFD GETYAVSGGL HGVGVSVVNA LSTRLEATVL RDGYEWFQYY 150
DRSVPGKLKQ GGETKETGTT IRFWADPEIF ETTDYNFETV ARRLQEMAFL 200
NKGLTIELTD ERVTAEEVVD DVVKDTAEAP KTADEKAAEA TGPSKVKHRV 250
FHYPGGLVDY VKHINRTKTP IQQSIIDFDG KGPGHEVEIA MQWNAGYSES 300
VHTFANTINT HEGGTHEEGF RAALTSVVNR YAKDKKLLKD KDPNLTGDDI 350
REGLAAVISV KVAEPQFEGQ TKTKLGNTEV KSFVQKICNE QLQHWFEANP 400
AEAKTVVNKA VSSAQARIAA RKARELVRRK SATDIGGLPG KLADCRSTDP 450
SKSELYVVEG DSAGGSAKSG RDSMFQAILP LRGKIINVEK ARIDRVLKNT 500
EVQSIITALG TGIHDEFDIS KLRYHKIVLM ADADVDGQHI STLLLTLLFR 550
FMKPLVENGH IFLAQPPLYK LKWQRSEPEF AYSDRERDGL LEAGRAAGKK 600
INVDDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI 650
LMGEDVEARR SFITRNAKDV RFLDV 675
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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti162 – 1621G → R in CAA58884. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X92503 Genomic DNA. Translation: CAA63253.1. Different initiation.
X84077 Genomic DNA. Translation: CAA58884.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X92503 Genomic DNA. Translation: CAA63253.1 . Different initiation.
X84077 Genomic DNA. Translation: CAA58884.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4B6C X-ray 2.20 A/B 9-255 [» ]
4BAE X-ray 2.35 A/B/C/D 19-212 [» ]
A/B/C/D 247-255 [» ]
ProteinModelPortali P0C559.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

Gene3Di 3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPi MF_01898. GyrB.
InterProi IPR002288. 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 ]
Pfami PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00418. TPI2FAMILY.
SMARTi SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsi TIGR01059. gyrB. 1 hit.
PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

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: July 9, 2014
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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