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P77966

- GYRB_SYNY3

UniProt

P77966 - GYRB_SYNY3

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Protein
DNA gyrase subunit B
Gene
gyrB, sll2005
Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

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 By similarity.

Catalytic activityi

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

Cofactori

Magnesium. Binds two Mg2+ per subunit By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi895 – 8951Magnesium 1; catalytic By similarity
Metal bindingi939 – 9391Magnesium 1; catalytic By similarity
Metal bindingi939 – 9391Magnesium 2 By similarity
Metal bindingi941 – 9411Magnesium 2 By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: InterPro
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-EC
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA topological change Source: InterPro
  2. intein-mediated protein splicing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit B (EC:5.99.1.3)
Cleaved into the following chain:
Gene namesi
Name:gyrB
Ordered Locus Names:sll2005
OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
Taxonomic identifieri1111708 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
ProteomesiUP000001425: Chromosome

Subcellular locationi

Cytoplasm Reviewed prediction

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
Chaini1 – 436436DNA gyrase subunit B, 1st part Reviewed prediction
PRO_0000034816Add
BLAST
Chaini437 – 871435Ssp gyrB intein Reviewed prediction
PRO_0000034817Add
BLAST
Chaini872 – 1078207DNA gyrase subunit B, 2nd part Reviewed prediction
PRO_0000034818Add
BLAST

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Reviewed prediction.

Proteomic databases

PaxDbiP77966.
PRIDEiP77966.

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.

Protein-protein interaction databases

DIPiDIP-48809N.
IntActiP77966. 15 interactions.
STRINGi1148.sll2005.

Structurei

3D structure databases

ProteinModelPortaliP77966.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini889 – 97486Toprim
Add
BLAST

Sequence similaritiesi

Contains 1 Toprim domain.

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075154.
KOiK02470.
OMAiNARWREV.
OrthoDBiEOG6P334W.
PhylomeDBiP77966.

Family and domain databases

Gene3Di2.170.16.10. 2 hits.
3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_ATP-bd.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR006141. Intein_splice_site.
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.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 2 hits.
SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00177. 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.

P77966-1 [UniParc]FASTAAdd to Basket

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MTMTTTNYGA DQIQVLEGLE PVRKRPGMYI GSTGPKGLHH LVYEVVDNAI     50
DEALAGYCTH IEIDINADGS VTVVDNGRGI PTDIHPTTGR SALETVLTVL 100
HAGGKFGGGG YKVSGGLHGV GVSVVNALSE WVEVKVWRQG KEHFQRFERG 150
NPIGTLEATP NEGHSTGTQV SFLPDTQIFK DGIEFDYHTL ASRLKELAYL 200
NAGVRITFGD RRADSLKEEQ FYYEGGIREY VTYMTTDKTP LHEEIIYTSG 250
EKNDVQVEVA LQWCVDAYSD TLLGFANNIR TIDGGTHLEG LKAVLTRTLN 300
SVARKRNKLK DGDSNLGGEN IREGLTGVIS VKVPDPEFEG QTKTKLGNTE 350
VRGIVDTLVG EALTEFLEFN PGVADAIIEK AVQAFKAAEA ARRARELVRR 400
KSVLESSTLP GKLADCSSKD PSESEIFIVE GDSAGGCFSG DTLVALTDGR 450
SVSFEQLVEE EKQGKQNFCY TIRHDGSIGV EKIINARKTK TNAKVIKVTL 500
DNGESIICTP DHKFMLRDGS YKCAMDLTLD DSLMPLHRKI STTEDSGITI 550
DGYEMVWSPR SDSWLFTHLV ADWYNRWQGI YIAEEKQHCH HKDFNKRNNN 600
PDNLIRLSPE KHLALHRKHI SKTLHRPDVV EKCRRIHQSP EFRRKMSARM 650
QSPETRAILS KQAQAQWQNE TYKLTMMESW RSFYDSNEDY RQQNAEQLNR 700
AQQEYWAQAE NRTAQAERVR QHFAQNPGLR QQYSENAVKQ WNNPELLKWR 750
QKKTKEQWTP EFREKRREAL AQTYYRKTLA ALKQVEIENG YLDISAYDSY 800
RISTKDKSLL RFDRFCERYF ENDENLAREA VLNYNHRIVN IEAVSETIDV 850
YDIEVPHTHN FALASGVFVH NSAKQGRDRR FQAILPLRGK ILNIEKTDDA 900
KIYKNTEIQA LITALGLGIK GDDFDISSLR YHRVVIMTDA DVDGAHIRTL 950
LLTFFYRYQR DLVDQGYIYI ACPPLYKLER GKNHFYCYSD RELQEQISQF 1000
PPNANYTIQR FKGLGEMMPQ QLWDTTMNPE SRTMKRVHIE DAAEADRIFT 1050
VLMGDRVAPR REFIETYGTK LDLTDLDI 1078
Length:1,078
Mass (Da):122,819
Last modified:February 1, 1997 - v1
Checksum:i6CA02586DFEA607B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000022 Genomic DNA. Translation: BAA17720.1.
PIRiS77162.
RefSeqiNP_441040.1. NC_000911.1.
YP_005651097.1. NC_017277.1.
YP_007450922.1. NC_020286.1.

Genome annotation databases

EnsemblBacteriaiBAA17720; BAA17720; BAA17720.
GeneIDi954353.
KEGGisyn:sll2005.
syy:SYNGTS_1144.
syz:MYO_111540.
PATRICi23839370. VBISynSp132158_1249.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000022 Genomic DNA. Translation: BAA17720.1 .
PIRi S77162.
RefSeqi NP_441040.1. NC_000911.1.
YP_005651097.1. NC_017277.1.
YP_007450922.1. NC_020286.1.

3D structure databases

ProteinModelPortali P77966.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-48809N.
IntActi P77966. 15 interactions.
STRINGi 1148.sll2005.

Proteomic databases

PaxDbi P77966.
PRIDEi P77966.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAA17720 ; BAA17720 ; BAA17720 .
GeneIDi 954353.
KEGGi syn:sll2005.
syy:SYNGTS_1144.
syz:MYO_111540.
PATRICi 23839370. VBISynSp132158_1249.

Phylogenomic databases

eggNOGi COG0187.
HOGENOMi HOG000075154.
KOi K02470.
OMAi NARWREV.
OrthoDBi EOG6P334W.
PhylomeDBi P77966.

Family and domain databases

Gene3Di 2.170.16.10. 2 hits.
3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
InterProi IPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_ATP-bd.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR006141. Intein_splice_site.
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.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view ]
SUPFAMi SSF51294. SSF51294. 2 hits.
SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsi TIGR01059. gyrB. 1 hit.
TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEi PS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
    Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
    , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 6803 / Kazusa.

Entry informationi

Entry nameiGYRB_SYNY3
AccessioniPrimary (citable) accession number: P77966
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: July 9, 2014
This is version 110 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

Complete proteome, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. SIMILARITY comments
    Index of protein domains and families
  3. Synechocystis PCC 6803
    Synechocystis (strain PCC 6803): entries and gene names

External Data

Dasty 3

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