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Protein

Phosphorelay intermediate protein YPD1

Gene

YPD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Phosphorelay intermediate protein that is part of the branched SLN1-YPD1-SKN7/SSK1 two-component regulatory system, which controls activity of the HOG1 pathway and gene expression in response to changes in the osmolarity of the extracellular environment. Catalyzes the phosphoryl group transfer from the membrane-bound osmosensing histidine kinase SLN1 to two distinct response regulator proteins, SSK1 in the cytoplasm, and transcription factor SKN7 in the nucleus.2 Publications

GO - Molecular functioni

  • protein histidine kinase binding Source: SGD
  • signal transducer activity Source: InterPro
  • transferase activity, transferring phosphorus-containing groups Source: SGD

GO - Biological processi

  • osmosensory signaling via phosphorelay pathway Source: SGD
Complete GO annotation...

Keywords - Biological processi

Two-component regulatory system

Enzyme and pathway databases

BioCyciYEAST:G3O-29613-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphorelay intermediate protein YPD1
Alternative name(s):
Histidine-containing phosphotransfer protein YPD1
Tyrosine phosphatase-dependent protein 1
Gene namesi
Name:YPD1
Ordered Locus Names:YDL235C
ORF Names:D0790
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL235C.
SGDiS000002394. YPD1.

Subcellular locationi

  • Cytoplasm
  • Nucleus

  • Note: Localizes constitutively to the cytoplasm and the nucleus, independent on osmotic conditions and phosphorylation status of the protein.

GO - Cellular componenti

  • cytoplasm Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi64 – 641H → Q: Loss of function. 1 Publication
Mutagenesisi67 – 671K → A: Reduces binding of the 4-aspartylphosphate of SLN1. 1 Publication
Mutagenesisi68 – 681G → Q: Reduces phosphoryl transfer rate. 1 Publication
Mutagenesisi74 – 741G → C in NH1; causes resistance to the antifungal antibiotic pradimicin. 1 Publication
Mutagenesisi86 – 861Q → A: Reduces phosphoryl transfer rate. 1 Publication
Mutagenesisi90 – 901R → A: Reduces phosphoryl transfer rate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 167167Phosphorelay intermediate protein YPD1PRO_0000262758Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei64 – 641PhosphohistidinePROSITE-ProRule annotation1 Publication

Post-translational modificationi

The phosphorelay mechanism involves the sequential transfer of a phosphate group from 'His-576' (H1) to 'Asp-1144' (D1) of SLN1, then to His-64 (H2) of YPD1 and finally to 'Asp-554' (D2) of SSK1 or 'Asp-427' (D2) of SKN7.

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ07688.
PeptideAtlasiQ07688.
TopDownProteomicsiQ07688.

PTM databases

iPTMnetiQ07688.

Interactioni

Subunit structurei

Interacts with the response regulatory domains of SLN1 and SSK1.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SLN1P399282EBI-34423,EBI-17357
SSK1Q070843EBI-34423,EBI-18184

GO - Molecular functioni

  • protein histidine kinase binding Source: SGD

Protein-protein interaction databases

BioGridi31876. 90 interactions.
DIPiDIP-5899N.
IntActiQ07688. 3 interactions.
MINTiMINT-696217.

Structurei

Secondary structure

1
167
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi11 – 199Combined sources
Turni20 – 234Combined sources
Helixi26 – 5126Combined sources
Helixi56 – 7217Combined sources
Helixi76 – 8914Combined sources
Helixi99 – 1035Combined sources
Helixi109 – 1124Combined sources
Beta strandi113 – 1153Combined sources
Turni117 – 1204Combined sources
Beta strandi128 – 1303Combined sources
Helixi135 – 16228Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1C02X-ray1.80A/B2-167[»]
1C03X-ray2.30A/B/C/D1-167[»]
1OXBX-ray2.30A2-167[»]
1OXKX-ray2.10A/C/E/G/I/K2-167[»]
1QSPX-ray2.70A/B3-167[»]
2R25X-ray1.70A1-167[»]
ProteinModelPortaliQ07688.
SMRiQ07688. Positions 2-167.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ07688.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini24 – 129106HPtPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the YPD1 family.Curated
Contains 1 HPt domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000190539.
InParanoidiQ07688.
KOiK11232.
OMAiAWACERI.
OrthoDBiEOG72894C.

Family and domain databases

Gene3Di1.20.120.160. 1 hit.
InterProiIPR008207. Sig_transdc_His_kin_Hpt_dom.
[Graphical view]
PfamiPF01627. Hpt. 1 hit.
[Graphical view]
SMARTiSM00073. HPT. 1 hit.
[Graphical view]
SUPFAMiSSF47226. SSF47226. 1 hit.
PROSITEiPS50894. HPT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q07688-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTIPSEIIN WTILNEIISM DDDDSDFSKG LIIQFIDQAQ TTFAQMQRQL
60 70 80 90 100
DGEKNLTELD NLGHFLKGSS AALGLQRIAW VCERIQNLGR KMEHFFPNKT
110 120 130 140 150
ELVNTLSDKS IINGINIDED DEEIKIQVDD KDENSIYLIL IAKALNQSRL
160
EFKLARIELS KYYNTNL
Length:167
Mass (Da):19,169
Last modified:November 1, 1996 - v1
Checksum:i4B923E621C57783D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U62016 Genomic DNA. Translation: AAC49440.1.
Z74283 Genomic DNA. Translation: CAA98815.1.
BK006938 Genomic DNA. Translation: DAA11631.1.
PIRiS67799.
RefSeqiNP_010046.1. NM_001180295.1.

Genome annotation databases

EnsemblFungiiYDL235C; YDL235C; YDL235C.
GeneIDi851363.
KEGGisce:YDL235C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U62016 Genomic DNA. Translation: AAC49440.1.
Z74283 Genomic DNA. Translation: CAA98815.1.
BK006938 Genomic DNA. Translation: DAA11631.1.
PIRiS67799.
RefSeqiNP_010046.1. NM_001180295.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1C02X-ray1.80A/B2-167[»]
1C03X-ray2.30A/B/C/D1-167[»]
1OXBX-ray2.30A2-167[»]
1OXKX-ray2.10A/C/E/G/I/K2-167[»]
1QSPX-ray2.70A/B3-167[»]
2R25X-ray1.70A1-167[»]
ProteinModelPortaliQ07688.
SMRiQ07688. Positions 2-167.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31876. 90 interactions.
DIPiDIP-5899N.
IntActiQ07688. 3 interactions.
MINTiMINT-696217.

PTM databases

iPTMnetiQ07688.

Proteomic databases

MaxQBiQ07688.
PeptideAtlasiQ07688.
TopDownProteomicsiQ07688.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL235C; YDL235C; YDL235C.
GeneIDi851363.
KEGGisce:YDL235C.

Organism-specific databases

EuPathDBiFungiDB:YDL235C.
SGDiS000002394. YPD1.

Phylogenomic databases

HOGENOMiHOG000190539.
InParanoidiQ07688.
KOiK11232.
OMAiAWACERI.
OrthoDBiEOG72894C.

Enzyme and pathway databases

BioCyciYEAST:G3O-29613-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ07688.
PROiQ07688.

Family and domain databases

Gene3Di1.20.120.160. 1 hit.
InterProiIPR008207. Sig_transdc_His_kin_Hpt_dom.
[Graphical view]
PfamiPF01627. Hpt. 1 hit.
[Graphical view]
SMARTiSM00073. HPT. 1 hit.
[Graphical view]
SUPFAMiSSF47226. SSF47226. 1 hit.
PROSITEiPS50894. HPT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Yeast HOG1 MAP kinase cascade is regulated by a multistep phosphorelay mechanism in the SLN1-YPD1-SSK1 two-component osmosensor."
    Posas F., Wurgler-Murphy S.M., Maeda T., Witten E.A., Thai T.C., Saito H.
    Cell 86:865-875(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF HIS-64, PHOSPHORYLATION AT HIS-64, INTERACTION WITH SLN1 AND SSK1.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [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. "The yeast histidine protein kinase, Sln1p, mediates phosphotransfer to two response regulators, Ssk1p and Skn7p."
    Li S., Ault A., Malone C.L., Raitt D., Dean S., Johnston L.H., Deschenes R.J., Fassler J.S.
    EMBO J. 17:6952-6962(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Novel role for an HPt domain in stabilizing the phosphorylated state of a response regulator domain."
    Janiak-Spens F., Sparling D.P., West A.H.
    J. Bacteriol. 182:6673-6678(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Pradimicin-resistance of yeast is caused by a point mutation of the histidine-containing phosphotransfer protein Ypd1."
    Hiramoto F., Nomura N., Furumai T., Igarashi Y., Oki T.
    J. Antibiot. 56:1053-1057(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLY-74.
  7. "Saccharomyces cerevisiae histidine phosphotransferase Ypd1p shuttles between the nucleus and cytoplasm for SLN1-dependent phosphorylation of Ssk1p and Skn7p."
    Lu J.M.-Y., Deschenes R.J., Fassler J.S.
    Eukaryot. Cell 2:1304-1314(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "Kinetic analysis of YPD1-dependent phosphotransfer reactions in the yeast osmoregulatory phosphorelay system."
    Janiak-Spens F., Cook P.F., West A.H.
    Biochemistry 44:377-386(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, MUTAGENESIS OF LYS-67; GLY-68; GLN-86 AND ARG-90.
  11. "Conservation of structure and function among histidine-containing phosphotransfer (HPt) domains as revealed by the crystal structure of YPD1."
    Xu Q., West A.H.
    J. Mol. Biol. 292:1039-1050(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 3-167.
  12. "Insights into eukaryotic multistep phosphorelay signal transduction revealed by the crystal structure of Ypd1p from Saccharomyces cerevisiae."
    Song H.K., Lee J.Y., Lee M.G., Moon J., Min K., Yang J.K., Suh S.W.
    J. Mol. Biol. 293:753-761(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
  13. "The yeast YPD1/SLN1 complex: insights into molecular recognition in two-component signaling systems."
    Xu Q., Porter S.W., West A.H.
    Structure 11:1569-1581(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-167 IN COMPLEX WITH SLN1.

Entry informationi

Entry nameiYPD1_YEAST
AccessioniPrimary (citable) accession number: Q07688
Secondary accession number(s): D6VRC1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 28, 2006
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 108 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 6330 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. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

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.