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P38197

- YBD6_YEAST

UniProt

P38197 - YBD6_YEAST

Protein

UPF0001 protein YBL036C

Gene

YBL036C

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 121 (01 Oct 2014)
      Sequence version 1 (01 Oct 1994)
      Previous versions | rss
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    Functioni

    Cofactori

    Pyridoxal phosphate.

    GO - Molecular functioni

    1. pyridoxal phosphate binding Source: SGD

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciYEAST:G3O-28938-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    UPF0001 protein YBL036C
    Gene namesi
    Ordered Locus Names:YBL036C
    ORF Names:YBL0413
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    CYGDiYBL036c.
    SGDiS000000132. YBL036C.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 257256UPF0001 protein YBL036CPRO_0000163213Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine1 Publication
    Modified residuei49 – 491N6-(pyridoxal phosphate)lysine

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP38197.
    PaxDbiP38197.
    PeptideAtlasiP38197.

    Expressioni

    Gene expression databases

    GenevestigatoriP38197.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself1EBI-21226,EBI-21226

    Protein-protein interaction databases

    BioGridi32661. 50 interactions.
    DIPiDIP-6608N.
    IntActiP38197. 4 interactions.
    MINTiMINT-624974.
    STRINGi4932.YBL036C.

    Structurei

    Secondary structure

    1
    257
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 3123
    Beta strandi43 – 475
    Helixi53 – 6210
    Beta strandi66 – 694
    Helixi72 – 8110
    Beta strandi87 – 904
    Helixi96 – 983
    Helixi99 – 1046
    Beta strandi108 – 1147
    Helixi117 – 13014
    Beta strandi132 – 1343
    Beta strandi137 – 1437
    Beta strandi146 – 1483
    Beta strandi151 – 1544
    Helixi157 – 16812
    Beta strandi174 – 1818
    Helixi197 – 21317
    Beta strandi218 – 2203
    Turni224 – 2263
    Helixi227 – 2326
    Beta strandi236 – 2416
    Helixi242 – 2454

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1B54X-ray2.10A1-257[»]
    1CT5X-ray2.00A2-257[»]
    ProteinModelPortaliP38197.
    SMRiP38197. Positions 4-246.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP38197.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the UPF0001 family.Curated

    Phylogenomic databases

    eggNOGiCOG0325.
    GeneTreeiENSGT00390000004928.
    HOGENOMiHOG000048983.
    KOiK06997.
    OMAiQVHIAKE.
    OrthoDBiEOG7VX96Z.

    Family and domain databases

    Gene3Di3.20.20.10. 1 hit.
    InterProiIPR001608. Ala_racemase_N.
    IPR029066. PLP-binding_barrel.
    IPR011078. UPF0001.
    [Graphical view]
    PANTHERiPTHR10146. PTHR10146. 1 hit.
    PfamiPF01168. Ala_racemase_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004848. YBL036c_PLPDEIII. 1 hit.
    SUPFAMiSSF51419. SSF51419. 1 hit.
    TIGRFAMsiTIGR00044. TIGR00044. 1 hit.
    PROSITEiPS01211. UPF0001. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P38197-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTGITYDED RKTQLIAQYE SVREVVNAEA KNVHVNENAS KILLLVVSKL    50
    KPASDIQILY DHGVREFGEN YVQELIEKAK LLPDDIKWHF IGGLQTNKCK 100
    DLAKVPNLYS VETIDSLKKA KKLNESRAKF QPDCNPILCN VQINTSHEDQ 150
    KSGLNNEAEI FEVIDFFLSE ECKYIKLNGL MTIGSWNVSH EDSKENRDFA 200
    TLVEWKKKID AKFGTSLKLS MGMSADFREA IRQGTAEVRI GTDIFGARPP 250
    KNEARII 257
    Length:257
    Mass (Da):29,123
    Last modified:October 1, 1994 - v1
    Checksum:i5643EE0D36B6D85A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti8 – 81D → G in AAT92893. (PubMed:17322287)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X78214 Genomic DNA. Translation: CAA55058.1.
    Z35797 Genomic DNA. Translation: CAA84856.1.
    AY692874 Genomic DNA. Translation: AAT92893.1.
    BK006936 Genomic DNA. Translation: DAA07083.1.
    PIRiS50294.
    RefSeqiNP_009517.1. NM_001178276.1.

    Genome annotation databases

    EnsemblFungiiYBL036C; YBL036C; YBL036C.
    GeneIDi852244.
    KEGGisce:YBL036C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X78214 Genomic DNA. Translation: CAA55058.1 .
    Z35797 Genomic DNA. Translation: CAA84856.1 .
    AY692874 Genomic DNA. Translation: AAT92893.1 .
    BK006936 Genomic DNA. Translation: DAA07083.1 .
    PIRi S50294.
    RefSeqi NP_009517.1. NM_001178276.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1B54 X-ray 2.10 A 1-257 [» ]
    1CT5 X-ray 2.00 A 2-257 [» ]
    ProteinModelPortali P38197.
    SMRi P38197. Positions 4-246.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32661. 50 interactions.
    DIPi DIP-6608N.
    IntActi P38197. 4 interactions.
    MINTi MINT-624974.
    STRINGi 4932.YBL036C.

    Proteomic databases

    MaxQBi P38197.
    PaxDbi P38197.
    PeptideAtlasi P38197.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YBL036C ; YBL036C ; YBL036C .
    GeneIDi 852244.
    KEGGi sce:YBL036C.

    Organism-specific databases

    CYGDi YBL036c.
    SGDi S000000132. YBL036C.

    Phylogenomic databases

    eggNOGi COG0325.
    GeneTreei ENSGT00390000004928.
    HOGENOMi HOG000048983.
    KOi K06997.
    OMAi QVHIAKE.
    OrthoDBi EOG7VX96Z.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-28938-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P38197.
    NextBioi 970802.
    PROi P38197.

    Gene expression databases

    Genevestigatori P38197.

    Family and domain databases

    Gene3Di 3.20.20.10. 1 hit.
    InterProi IPR001608. Ala_racemase_N.
    IPR029066. PLP-binding_barrel.
    IPR011078. UPF0001.
    [Graphical view ]
    PANTHERi PTHR10146. PTHR10146. 1 hit.
    Pfami PF01168. Ala_racemase_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF004848. YBL036c_PLPDEIII. 1 hit.
    SUPFAMi SSF51419. SSF51419. 1 hit.
    TIGRFAMsi TIGR00044. TIGR00044. 1 hit.
    PROSITEi PS01211. UPF0001. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The sequence of a 22.4 kb DNA fragment from the left arm of yeast chromosome II reveals homologues to bacterial proline synthetase and murine alpha-adaptin, as well as a new permease and a DNA-binding protein."
      de Wergifosse P., Jacques B., Jonniaux J.-L., Purnelle B., Skala J., Goffeau A.
      Yeast 10:1489-1496(1994) [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.
      , 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. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    6. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    7. "Structure of a yeast hypothetical protein selected by a structural genomics approach."
      Eswaramoorthy S., Gerchman S., Graziano V., Kycia H., Studier W., Swaminathan S.
      Acta Crystallogr. D 59:127-135(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH COFACTOR, PYRIDOXAL PHOSPHATE AT LYS-49.
      Strain: ATCC 204508 / S288c.

    Entry informationi

    Entry nameiYBD6_YEAST
    AccessioniPrimary (citable) accession number: P38197
    Secondary accession number(s): D6VPW3, Q6B256
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 121 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 4890 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome II
      Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

    External Data

    Dasty 3