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UniProtKB - D7CPP1 (D7CPP1_SYNLT)

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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Syntrophothermus lipocalidus (strain DSM 12680 / TGB-C1)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.UniRule annotation

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

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • Mg2+SAAS annotation
  • Mn2+SAAS annotation

GO - Molecular functioni

Complete GO annotation...

GO - Biological processi

Complete GO annotation...

Keywordsi

Molecular functionDNA-bindingSAAS annotation, Isomerase, TopoisomeraseUniRule annotationSAAS annotation
LigandATP-bindingUniRule annotationSAAS annotation, MagnesiumSAAS annotation, Metal-bindingSAAS annotation, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotationSAAS annotation (EC:5.99.1.3UniRule annotationSAAS annotation)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:Slip_0005Imported
OrganismiSyntrophothermus lipocalidus (strain DSM 12680 / TGB-C1)Imported
Taxonomic identifieri643648 [NCBI]
Taxonomic lineageiBacteria › Firmicutes › Clostridia › Clostridiales › Syntrophomonadaceae › Syntrophothermus ›
Proteomesi
  • UP000000378 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotation

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains. 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 annotation

Protein-protein interaction databases

STRINGi643648.Slip_0005.

Structurei

3D structure databases

ProteinModelPortaliD7CPP1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini421 – 535ToprimInterPro annotationAdd BLAST115

Sequence similaritiesi

Belongs to the type II topoisomerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075154.
KOiK02470.
OMAiDCSSRDP.
OrthoDBiPOG091H01XP.

Family and domain databases

CDDicd03366. TOPRIM_TopoIIA_GyrB. 1 hit.
Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiView protein in InterPro
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.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. TOPRIM_domain.
IPR034160. TOPRIM_GyrB.
PANTHERiPTHR10169. PTHR10169. 1 hit.
PfamiView protein in Pfam
PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
PRINTSiPR00418. TPI2FAMILY.
SMARTiView protein in SMART
SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiView protein in PROSITE
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.

Sequencei

Sequence statusi: Complete.

D7CPP1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNINGSKNEY TALDIQVLEG LEAVRKRPGM YIGSTDSRGL HHLVFEIVDN 
        60         70         80         90        100
SIDEAVAGYC DEIKVIILDD STVTVTDNGR GIPVDMHPKM GIPALEVILT 
       110        120        130        140        150
TLHSGAKFGG SGYTISGGLH GVGLSVVNAL SRWLEVEVAR DGQLYHQRYE 
       160        170        180        190        200
RGKPVTPLAV TGACQTTGTK ITFSPDPEIF EEICFSAEII GQRLRELSYL 
       210        220        230        240        250
NQGTRIVLCD KRTGRDVEYY HTGGIRDFVK YLSKNREPLS PEPIYFRIGK 
       260        270        280        290        300
EGTVVEVAIQ YNTGYTETLL SYANNIHTQE GGTHELGFKN GLTRVVNEYA 
       310        320        330        340        350
KKQGMLKENE GNLLGEDIRE GMTAVISVLV QDPQFEGQTK TKLGNAFIRS 
       360        370        380        390        400
LVEGAVSDFV GAFFDENPSL AKKIVEKAIA ARRAREAARK ARELTRRKNL 
       410        420        430        440        450
LDSTSLPGKL ADCSEKDPAL SELYLVEGDS AGGSAKQGRD RNFQAILPLR 
       460        470        480        490        500
GKILNVEKAR LDKVLSNEEI RALITAIGTG IGEDFDINKA RYHRLIIMTD 
       510        520        530        540        550
ADVDGSHIRV LLLTFFYRYM RPLIEAGYVY VAQPPLYELK RGKEVHYIYN 
       560        570        580        590        600
DRELQRFLEQ QGNKKYGVKR YKGLGEMNPE QLWETTMNPE NRTLLQVRIE 
       610        620        630 
DAIAADVIFS SLMGEKVEPR REFIQENARL VTNLDI
Length:636
Mass (Da):71,076
Last modified:August 10, 2010 - v1
Checksum:i0799A7E8050557BF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002048 Genomic DNA. Translation: ADI00813.1.
RefSeqiWP_013174217.1. NC_014220.1.

Genome annotation databases

EnsemblBacteriaiADI00813; ADI00813; Slip_0005.
KEGGislp:Slip_0005.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002048 Genomic DNA. Translation: ADI00813.1.
RefSeqiWP_013174217.1. NC_014220.1.

3D structure databases

ProteinModelPortaliD7CPP1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi643648.Slip_0005.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADI00813; ADI00813; Slip_0005.
KEGGislp:Slip_0005.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075154.
KOiK02470.
OMAiDCSSRDP.
OrthoDBiPOG091H01XP.

Family and domain databases

CDDicd03366. TOPRIM_TopoIIA_GyrB. 1 hit.
Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB. 1 hit.
InterProiView protein in InterPro
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.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. TOPRIM_domain.
IPR034160. TOPRIM_GyrB.
PANTHERiPTHR10169. PTHR10169. 1 hit.
PfamiView protein in Pfam
PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
PRINTSiPR00418. TPI2FAMILY.
SMARTiView protein in SMART
SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiView protein in PROSITE
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiD7CPP1_SYNLT
AccessioniPrimary (citable) accession number: D7CPP1
Entry historyiIntegrated into UniProtKB/TrEMBL: August 10, 2010
Last sequence update: August 10, 2010
Last modified: June 7, 2017
This is version 60 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.