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P34220 (YBF5_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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:
Deoxyribonuclease Tat-D

EC=3.1.21.-
Gene names
Ordered Locus Names:YBL055C
ORF Names:YBL0511, YBL0512
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length418 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Has both endo- and exonuclease activities. Incises double-stranded DNA without obvious specificity via its endonuclease activity and excises the DNA from the 3'-to 5'-end by its exonuclease activity. May have a role in apoptosis. Ref.7

Cofactor

Divalent metal cations. Has optimal activity with magnesium. Ref.7

Subcellular location

Cytoplasm Ref.5.

Miscellaneous

Present with 1460 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the TatD DNase family.

Biophysicochemical properties

pH dependence:

Optimum pH is 5. Ref.7

Temperature dependence:

Optimum temperature is 30 degrees Celsius.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 418418Deoxyribonuclease Tat-D
PRO_0000201994

Sites

Metal binding1851Divalent metal cation 1 By similarity
Metal binding1851Divalent metal cation 2 By similarity
Metal binding2261Divalent metal cation 2 By similarity
Metal binding2771Divalent metal cation 2 By similarity
Metal binding3271Divalent metal cation 1 By similarity

Experimental info

Mutagenesis1851E → A: Reduces enzymatic activities by 50%. Ref.7
Mutagenesis3251E → A: Reduces enzymatic activities by 50%. Ref.7
Mutagenesis3271D → A: Reduces enzymatic activities by almost 95%. Ref.7
Sequence conflict2781S → P in AAT92645. Ref.4

Sequences

Sequence LengthMass (Da)Tools
P34220 [UniParc].

Last modified February 1, 1994. Version 1.
Checksum: F1107C1B8E94CAD1

FASTA41847,390
        10         20         30         40         50         60 
MWGILLKSSN KSCSRLWKPI LTQYYSMTST ATDSPLKYYD IGLNLTDPMF HGIYNGKQYH 

        70         80         90        100        110        120 
PADYVKLLER AAQRHVKNAL VTGSSIAESQ SAIELVSSVK DLSPLKLYHT IGVHPCCVNE 

       130        140        150        160        170        180 
FADASQGDKA SASIDNPSMD EAYNESLYAK VISNPSFAQG KLKELYDLMN QQAKPHDTSF 

       190        200        210        220        230        240 
RSIGEIGLDY DRFHYSSKEM QKVFFEEQLK ISCLNDKLSS YPLFLHMRSA CDDFVQILER 

       250        260        270        280        290        300 
FIAGFTDERD TFQLQKLGAS SSSGFYKFHP DRKLVVHSFT GSAIDLQKLL NLSPNIFIGV 

       310        320        330        340        350        360 
NGCSLRTEEN LAVVKQIPTE RLLLETDAPW CEIKRTHASF QYLAKYQEVR DFEYPAFKSV 

       370        380        390        400        410 
KKNKLADKLN AEELYMVKGR NEPCNMEQVA IVVSEVKDVD LATLIDTTWK TTCKIFGE 

« Hide

References

« Hide 'large scale' references
[1]"Sequencing and functional analysis of a 32,560 bp segment on the left arm of yeast chromosome II. Identification of 26 open reading frames, including the KIP1 and SEC17 genes."
Scherens B., el Bakkoury M., Vierendeels F., Dubois E., Messenguy F.
Yeast 9:1355-1371(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"Complete DNA sequence of yeast chromosome II."
Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. expand/collapse author list , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[6]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]"Search for apoptotic nucleases in yeast: role of Tat-D nuclease in apoptotic DNA degradation."
Qiu J., Yoon J.H., Shen B.
J. Biol. Chem. 280:15370-15379(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLU-185; GLU-325 AND ASP-327.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z23261 Genomic DNA. Translation: CAA80792.1.
Z35816 Genomic DNA. Translation: CAA84875.1.
AY692626 Genomic DNA. Translation: AAT92645.1.
BK006936 Genomic DNA. Translation: DAA07065.1.
PIRS39833.
RefSeqNP_009498.1. NM_001178295.1.

3D structure databases

ProteinModelPortalP34220.
SMRP34220. Positions 35-417.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32644. 24 interactions.
MINTMINT-2492113.
STRING4932.YBL055C.

Proteomic databases

MaxQBP34220.
PaxDbP34220.
PeptideAtlasP34220.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYBL055C; YBL055C; YBL055C.
GeneID852225.
KEGGsce:YBL055C.

Organism-specific databases

CYGDYBL055c.
SGDS000000151. YBL055C.

Phylogenomic databases

eggNOGCOG0084.
GeneTreeENSGT00720000108776.
HOGENOMHOG000201523.
KOK03424.
OMARYIDIGI.
OrthoDBEOG7PZS7D.

Enzyme and pathway databases

BioCycYEAST:G3O-28953-MONOMER.

Gene expression databases

GenevestigatorP34220.

Family and domain databases

InterProIPR018228. DNase_TatD-rel_CS.
IPR001130. TatD_family.
[Graphical view]
PANTHERPTHR10060. PTHR10060. 1 hit.
PfamPF01026. TatD_DNase. 1 hit.
[Graphical view]
PROSITEPS01090. TATD_2. 1 hit.
PS01091. TATD_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio970751.
PROP34220.

Entry information

Entry nameYBF5_YEAST
AccessionPrimary (citable) accession number: P34220
Secondary accession number(s): D6VPU5, Q6B2V4
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: May 14, 2014
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families