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P17967

- PDI_YEAST

UniProt

P17967 - PDI_YEAST

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Protein

Protein disulfide-isomerase

Gene

PDI1

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

Functioni

Protein disulfide isomerase of ER lumen required for formation of disulfide bonds in secretory and cell-surface proteins and which unscrambles non-native disulfide bonds. Forms a complex with MNL1 to process unfolded protein-bound Man8GlcNAc2 oligosaccharides to Man7GlcNAc2, promoting degradation in unfolded protein response.3 Publications

Catalytic activityi

Catalyzes the rearrangement of -S-S- bonds in proteins.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei61 – 611NucleophileBy similarity
Sitei62 – 621Contributes to redox potential valueBy similarity
Sitei63 – 631Contributes to redox potential valueBy similarity
Active sitei64 – 641NucleophileBy similarity
Sitei126 – 1261Lowers pKa of C-terminal Cys of first active siteBy similarity
Active sitei406 – 4061NucleophileBy similarity
Sitei407 – 4071Contributes to redox potential valueBy similarity
Sitei408 – 4081Contributes to redox potential valueBy similarity
Active sitei409 – 4091NucleophileBy similarity
Sitei471 – 4711Lowers pKa of C-terminal Cys of second active siteBy similarity

GO - Molecular functioni

  1. protein disulfide isomerase activity Source: SGD
  2. protein disulfide oxidoreductase activity Source: SGD
  3. unfolded protein binding Source: SGD

GO - Biological processi

  1. cell redox homeostasis Source: InterPro
  2. oxidation-reduction process Source: GOC
  3. protein folding Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Enzyme and pathway databases

BioCyciYEAST:YCL043C-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein disulfide-isomerase (EC:5.3.4.1)
Short name:
PDI
Alternative name(s):
Thioredoxin-related glycoprotein 1
Gene namesi
Name:PDI1
Synonyms:MFP1, TRG1
Ordered Locus Names:YCL043C
ORF Names:YCL313, YCL43C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome III

Organism-specific databases

CYGDiYCL043c.
SGDiS000000548. PDI1.

Subcellular locationi

Endoplasmic reticulum lumen PROSITE-ProRule annotation

GO - Cellular componenti

  1. endoplasmic reticulum lumen Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2828Or 22Sequence AnalysisAdd
BLAST
Chaini29 – 522494Protein disulfide-isomerasePRO_0000034218Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi61 ↔ 64Redox-active1 PublicationPROSITE-ProRule annotation
Glycosylationi82 – 821N-linked (GlcNAc...)Sequence Analysis
Glycosylationi117 – 1171N-linked (GlcNAc...)Sequence Analysis
Glycosylationi155 – 1551N-linked (GlcNAc...)Sequence Analysis
Glycosylationi174 – 1741N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi406 ↔ 409Redox-active1 PublicationPROSITE-ProRule annotation
Glycosylationi425 – 4251N-linked (GlcNAc...)Sequence Analysis

Post-translational modificationi

The N-terminus is blocked.

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiP17967.
PaxDbiP17967.
PeptideAtlasiP17967.

Expressioni

Gene expression databases

GenevestigatoriP17967.

Interactioni

Subunit structurei

Interacts with EPS1, KAR2 and MNL1.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RNASE1P618232EBI-13012,EBI-908364From a different organism.

Protein-protein interaction databases

BioGridi30941. 162 interactions.
DIPiDIP-4978N.
IntActiP17967. 10 interactions.
MINTiMINT-497035.
STRINGi4932.YCL043C.

Structurei

Secondary structure

1
522
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni39 – 413Combined sources
Helixi42 – 465Combined sources
Beta strandi50 – 578Combined sources
Helixi62 – 7716Combined sources
Turni78 – 825Combined sources
Beta strandi84 – 896Combined sources
Turni90 – 923Combined sources
Helixi94 – 996Combined sources
Beta strandi104 – 1129Combined sources
Beta strandi119 – 1213Combined sources
Helixi128 – 13811Combined sources
Beta strandi142 – 1454Combined sources
Helixi149 – 1557Combined sources
Beta strandi162 – 1687Combined sources
Helixi171 – 18313Combined sources
Turni184 – 1874Combined sources
Beta strandi189 – 1946Combined sources
Beta strandi201 – 2066Combined sources
Beta strandi209 – 2157Combined sources
Helixi220 – 2234Combined sources
Helixi226 – 23611Combined sources
Helixi246 – 2549Combined sources
Beta strandi259 – 2668Combined sources
Helixi267 – 28317Combined sources
Turni284 – 2874Combined sources
Beta strandi289 – 2946Combined sources
Helixi295 – 2984Combined sources
Helixi301 – 3044Combined sources
Beta strandi311 – 3188Combined sources
Turni319 – 3224Combined sources
Beta strandi323 – 3264Combined sources
Helixi332 – 3365Combined sources
Helixi346 – 35813Combined sources
Beta strandi377 – 3815Combined sources
Turni383 – 3853Combined sources
Helixi386 – 3916Combined sources
Beta strandi397 – 4026Combined sources
Helixi407 – 42620Combined sources
Beta strandi431 – 4366Combined sources
Helixi437 – 4393Combined sources
Beta strandi448 – 4569Combined sources
Helixi473 – 48311Combined sources
Helixi490 – 50112Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2B5EX-ray2.40A23-522[»]
3BOAX-ray3.70A23-522[»]
ProteinModelPortaliP17967.
SMRiP17967. Positions 23-494.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP17967.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini29 – 141113Thioredoxin 1PROSITE-ProRule annotationAdd
BLAST
Domaini356 – 485130Thioredoxin 2PROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi519 – 5224Prevents secretion from ER

Sequence similaritiesi

Belongs to the protein disulfide isomerase family.Curated
Contains 2 thioredoxin domains.PROSITE-ProRule annotation

Keywords - Domaini

Redox-active center, Repeat, Signal

Phylogenomic databases

eggNOGiCOG0526.
GeneTreeiENSGT00760000119201.
HOGENOMiHOG000162459.
InParanoidiP17967.
KOiK09580.
OMAiHTNNDVD.
OrthoDBiEOG71CFZN.

Family and domain databases

Gene3Di3.40.30.10. 2 hits.
InterProiIPR005792. Prot_disulphide_isomerase.
IPR012336. Thioredoxin-like_fold.
IPR017937. Thioredoxin_CS.
IPR013766. Thioredoxin_domain.
[Graphical view]
PfamiPF00085. Thioredoxin. 2 hits.
[Graphical view]
SUPFAMiSSF52833. SSF52833. 4 hits.
TIGRFAMsiTIGR01130. ER_PDI_fam. 1 hit.
PROSITEiPS00014. ER_TARGET. 1 hit.
PS00194. THIOREDOXIN_1. 2 hits.
PS51352. THIOREDOXIN_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P17967-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKFSAGAVLS WSSLLLASSV FAQQEAVAPE DSAVVKLATD SFNEYIQSHD
60 70 80 90 100
LVLAEFFAPW CGHCKNMAPE YVKAAETLVE KNITLAQIDC TENQDLCMEH
110 120 130 140 150
NIPGFPSLKI FKNSDVNNSI DYEGPRTAEA IVQFMIKQSQ PAVAVVADLP
160 170 180 190 200
AYLANETFVT PVIVQSGKID ADFNATFYSM ANKHFNDYDF VSAENADDDF
210 220 230 240 250
KLSIYLPSAM DEPVVYNGKK ADIADADVFE KWLQVEALPY FGEIDGSVFA
260 270 280 290 300
QYVESGLPLG YLFYNDEEEL EEYKPLFTEL AKKNRGLMNF VSIDARKFGR
310 320 330 340 350
HAGNLNMKEQ FPLFAIHDMT EDLKYGLPQL SEEAFDELSD KIVLESKAIE
360 370 380 390 400
SLVKDFLKGD ASPIVKSQEI FENQDSSVFQ LVGKNHDEIV NDPKKDVLVL
410 420 430 440 450
YYAPWCGHCK RLAPTYQELA DTYANATSDV LIAKLDHTEN DVRGVVIEGY
460 470 480 490 500
PTIVLYPGGK KSESVVYQGS RSLDSLFDFI KENGHFDVDG KALYEEAQEK
510 520
AAEEADADAE LADEEDAIHD EL
Length:522
Mass (Da):58,227
Last modified:March 1, 1992 - v2
Checksum:i69CF3E05D7F74C94
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti33 – 5220AVVKL…SHDLV → LSLSWPPTLSMNTFSRTTWW in AAA34848. (PubMed:1840696)CuratedAdd
BLAST
Sequence conflicti83 – 831I → V in CAA36550. (PubMed:1761554)Curated
Sequence conflicti83 – 831I → V in AAA35169. (PubMed:1761554)Curated
Sequence conflicti114 – 1141S → R in CAA38402. (PubMed:1761235)Curated
Sequence conflicti143 – 1431V → S(PubMed:1761554)Curated
Sequence conflicti146 – 1461Missing(PubMed:1761554)Curated
Sequence conflicti168 – 1681K → E in CAA36550. (PubMed:1761554)Curated
Sequence conflicti168 – 1681K → E in AAA35169. (PubMed:1761554)Curated
Sequence conflicti197 – 1971D → E in AAA34848. (PubMed:1840696)Curated
Sequence conflicti215 – 2151V → R AA sequence (PubMed:1761527)Curated
Sequence conflicti226 – 2261A → V in CAA36550. (PubMed:1761554)Curated
Sequence conflicti226 – 2261A → V in AAA35169. (PubMed:1761554)Curated
Sequence conflicti333 – 3331E → S AA sequence (PubMed:1761527)Curated
Sequence conflicti351 – 3511S → P in AAA34848. (PubMed:1840696)Curated
Sequence conflicti455 – 4551L → F in AAA34848. (PubMed:1840696)Curated
Sequence conflicti458 – 4581G → S in CAA36550. (PubMed:1761554)Curated
Sequence conflicti458 – 4581G → S in AAA35169. (PubMed:1761554)Curated
Sequence conflicti505 – 5051A → AEADAEAEA(PubMed:1761554)Curated
Sequence conflicti505 – 5051A → AEADAEAEA(PubMed:1761235)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D00842 Genomic DNA. Translation: BAA00723.1.
X57712 Genomic DNA. Translation: CAA40883.1.
M62815 Genomic DNA. Translation: AAA34848.1.
X52313 Genomic DNA. Translation: CAA36550.1.
M76982 Genomic DNA. Translation: AAA35169.1.
X54535 Genomic DNA. Translation: CAA38402.1.
X59720 Genomic DNA. Translation: CAA42373.1.
BK006937 Genomic DNA. Translation: DAA07442.1.
PIRiJX0182. ISBYSS.
RefSeqiNP_009887.1. NM_001178688.1.

Genome annotation databases

EnsemblFungiiYCL043C; YCL043C; YCL043C.
GeneIDi850314.
KEGGisce:YCL043C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D00842 Genomic DNA. Translation: BAA00723.1 .
X57712 Genomic DNA. Translation: CAA40883.1 .
M62815 Genomic DNA. Translation: AAA34848.1 .
X52313 Genomic DNA. Translation: CAA36550.1 .
M76982 Genomic DNA. Translation: AAA35169.1 .
X54535 Genomic DNA. Translation: CAA38402.1 .
X59720 Genomic DNA. Translation: CAA42373.1 .
BK006937 Genomic DNA. Translation: DAA07442.1 .
PIRi JX0182. ISBYSS.
RefSeqi NP_009887.1. NM_001178688.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2B5E X-ray 2.40 A 23-522 [» ]
3BOA X-ray 3.70 A 23-522 [» ]
ProteinModelPortali P17967.
SMRi P17967. Positions 23-494.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 30941. 162 interactions.
DIPi DIP-4978N.
IntActi P17967. 10 interactions.
MINTi MINT-497035.
STRINGi 4932.YCL043C.

Proteomic databases

MaxQBi P17967.
PaxDbi P17967.
PeptideAtlasi P17967.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YCL043C ; YCL043C ; YCL043C .
GeneIDi 850314.
KEGGi sce:YCL043C.

Organism-specific databases

CYGDi YCL043c.
SGDi S000000548. PDI1.

Phylogenomic databases

eggNOGi COG0526.
GeneTreei ENSGT00760000119201.
HOGENOMi HOG000162459.
InParanoidi P17967.
KOi K09580.
OMAi HTNNDVD.
OrthoDBi EOG71CFZN.

Enzyme and pathway databases

BioCyci YEAST:YCL043C-MONOMER.

Miscellaneous databases

EvolutionaryTracei P17967.
NextBioi 965715.
PROi P17967.

Gene expression databases

Genevestigatori P17967.

Family and domain databases

Gene3Di 3.40.30.10. 2 hits.
InterProi IPR005792. Prot_disulphide_isomerase.
IPR012336. Thioredoxin-like_fold.
IPR017937. Thioredoxin_CS.
IPR013766. Thioredoxin_domain.
[Graphical view ]
Pfami PF00085. Thioredoxin. 2 hits.
[Graphical view ]
SUPFAMi SSF52833. SSF52833. 4 hits.
TIGRFAMsi TIGR01130. ER_PDI_fam. 1 hit.
PROSITEi PS00014. ER_TARGET. 1 hit.
PS00194. THIOREDOXIN_1. 2 hits.
PS51352. THIOREDOXIN_2. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular structure of a yeast gene, PDI1, encoding protein disulfide isomerase that is essential for cell growth."
    Tachikawa H., Miura T., Katakura Y., Mizunaga T.
    J. Biochem. 110:306-313(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: ATCC 26786 / X2180-1A and TM5.
  2. "Determination of the sequence of the yeast YCL313 gene localized on chromosome III. Homology with the protein disulfide isomerase (PDI gene product) of other organisms."
    Scherens B., Dubois E., Messenguy F.
    Yeast 7:185-193(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Glycosylation site binding protein and protein disulfide isomerase are identical and essential for cell viability in yeast."
    Lamantia M., Miura T., Tachikawa H., Kaplan H.A., Lennarz W.J., Mizunaga T.
    Proc. Natl. Acad. Sci. U.S.A. 88:4453-4457(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The Saccharomyces cerevisiae TRG1 gene is essential for growth and encodes a lumenal endoplasmic reticulum glycoprotein involved in the maturation of vacuolar carboxypeptidase."
    Guenther R., Braeuer C., Janetzky B., Foerster H.H., Ehbrecht I.M., Lehle L., Kuentzel H.
    J. Biol. Chem. 266:24557-24563(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  5. "Protein disulfide isomerase is essential for viability in Saccharomyces cerevisiae."
    Farquhar R., Honey N., Murant S.J., Bossier P., Schultz L., Montogomery D., Ellis R.W., Freedman R.B., Tuite M.F.
    Gene 108:81-89(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  6. "The complete sequence of a 9,543 bp segment on the left arm of chromosome III reveals five open reading frames including glucokinase and the protein disulfide isomerase."
    Scherens B., Messenguy F., Gigot D., Dubois E.
    Yeast 8:577-586(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  7. "The complete DNA sequence of yeast chromosome III."
    Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
    , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
    Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  8. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  9. "Interactions among yeast protein-disulfide isomerase proteins and endoplasmic reticulum chaperone proteins influence their activities."
    Kimura T., Hosoda Y., Sato Y., Kitamura Y., Ikeda T., Horibe T., Kikuchi M.
    J. Biol. Chem. 280:31438-31441(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH EPS1 AND KAR2.
  10. "Htm1 protein generates the N-glycan signal for glycoprotein degradation in the endoplasmic reticulum."
    Clerc S., Hirsch C., Oggier D.M., Deprez P., Jakob C., Sommer T., Aebi M.
    J. Cell Biol. 184:159-172(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH MNL1.
  11. "A complex of Pdi1p and the mannosidase Htm1p initiates clearance of unfolded glycoproteins from the endoplasmic reticulum."
    Gauss R., Kanehara K., Carvalho P., Ng D.T., Aebi M.
    Mol. Cell 42:782-793(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH MNL1.
  12. "The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites."
    Tian G., Xiang S., Noiva R., Lennarz W.J., Schindelin H.
    Cell 124:61-73(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 23-522, DISULFIDE BONDS.

Entry informationi

Entry nameiPDI_YEAST
AccessioniPrimary (citable) accession number: P17967
Secondary accession number(s): D6VQX3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: March 1, 1992
Last modified: November 26, 2014
This is version 151 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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 III
    Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

External Data

Dasty 3