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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.

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+.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi459 – 4591Magnesium 1; catalyticUniRule annotation
Sitei484 – 4841Interaction with DNAUniRule annotation
Sitei487 – 4871Interaction with DNAUniRule annotation
Metal bindingi532 – 5321Magnesium 1; catalyticUniRule annotation
Metal bindingi532 – 5321Magnesium 2UniRule annotation
Metal bindingi534 – 5341Magnesium 2UniRule annotation

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-dependent DNA replication Source: UniProtKB-HAMAP
  2. DNA topological change Source: InterPro
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 lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 675674DNA gyrase subunit BPRO_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.UniRule annotation

Structurei

Secondary structure

1
675
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.
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 family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

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.
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 [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.

Experimental Info

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

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...

Chemistry

ChEMBLi CHEMBL3085613.

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_C.
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: October 29, 2014
This is version 42 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