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P38197

- YBD6_YEAST

UniProt

P38197 - YBD6_YEAST

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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

Functioni

Cofactori

Pyridoxal phosphate.

GO - Molecular functioni

  1. pyridoxal phosphate binding Source: SGD
Complete GO annotation...

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. 51 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.
InParanoidiP38197.
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 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSTGITYDED RKTQLIAQYE SVREVVNAEA KNVHVNENAS KILLLVVSKL
60 70 80 90 100
KPASDIQILY DHGVREFGEN YVQELIEKAK LLPDDIKWHF IGGLQTNKCK
110 120 130 140 150
DLAKVPNLYS VETIDSLKKA KKLNESRAKF QPDCNPILCN VQINTSHEDQ
160 170 180 190 200
KSGLNNEAEI FEVIDFFLSE ECKYIKLNGL MTIGSWNVSH EDSKENRDFA
210 220 230 240 250
TLVEWKKKID AKFGTSLKLS MGMSADFREA IRQGTAEVRI GTDIFGARPP

KNEARII
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. 51 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.
InParanoidi P38197.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 122 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