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P17967

- PDI_YEAST

UniProt

P17967 - PDI_YEAST

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Protein

Protein disulfide-isomerase

Gene
PDI1, MFP1, TRG1, YCL043C, YCL313, YCL43C
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 – 611Nucleophile By similarity
Sitei62 – 621Contributes to redox potential value By similarity
Sitei63 – 631Contributes to redox potential value By similarity
Active sitei64 – 641Nucleophile By similarity
Sitei126 – 1261Lowers pKa of C-terminal Cys of first active site By similarity
Active sitei406 – 4061Nucleophile By similarity
Sitei407 – 4071Contributes to redox potential value By similarity
Sitei408 – 4081Contributes to redox potential value By similarity
Active sitei409 – 4091Nucleophile By similarity
Sitei471 – 4711Lowers pKa of C-terminal Cys of second active site By similarity

GO - Molecular functioni

  1. protein binding Source: IntAct
  2. protein disulfide isomerase activity Source: SGD
  3. protein disulfide oxidoreductase activity Source: SGD
  4. 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 Reviewed prediction

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 22 Reviewed predictionAdd
BLAST
Chaini29 – 522494Protein disulfide-isomerasePRO_0000034218Add
BLAST

Amino acid modifications

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

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

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP17967.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini29 – 141113Thioredoxin 1Add
BLAST
Domaini356 – 485130Thioredoxin 2Add
BLAST

Motif

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

Sequence similaritiesi

Contains 2 thioredoxin domains.

Keywords - Domaini

Redox-active center, Repeat, Signal

Phylogenomic databases

eggNOGiCOG0526.
GeneTreeiENSGT00740000115037.
HOGENOMiHOG000162459.
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

MKFSAGAVLS WSSLLLASSV FAQQEAVAPE DSAVVKLATD SFNEYIQSHD    50
LVLAEFFAPW CGHCKNMAPE YVKAAETLVE KNITLAQIDC TENQDLCMEH 100
NIPGFPSLKI FKNSDVNNSI DYEGPRTAEA IVQFMIKQSQ PAVAVVADLP 150
AYLANETFVT PVIVQSGKID ADFNATFYSM ANKHFNDYDF VSAENADDDF 200
KLSIYLPSAM DEPVVYNGKK ADIADADVFE KWLQVEALPY FGEIDGSVFA 250
QYVESGLPLG YLFYNDEEEL EEYKPLFTEL AKKNRGLMNF VSIDARKFGR 300
HAGNLNMKEQ FPLFAIHDMT EDLKYGLPQL SEEAFDELSD KIVLESKAIE 350
SLVKDFLKGD ASPIVKSQEI FENQDSSVFQ LVGKNHDEIV NDPKKDVLVL 400
YYAPWCGHCK RLAPTYQELA DTYANATSDV LIAKLDHTEN DVRGVVIEGY 450
PTIVLYPGGK KSESVVYQGS RSLDSLFDFI KENGHFDVDG KALYEEAQEK 500
AAEEADADAE LADEEDAIHD EL 522
Length:522
Mass (Da):58,227
Last modified:March 1, 1992 - v2
Checksum:i69CF3E05D7F74C94
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti33 – 5220AVVKL…SHDLV → LSLSWPPTLSMNTFSRTTWW in AAA34848. 1 PublicationAdd
BLAST
Sequence conflicti83 – 831I → V in CAA36550. 1 Publication
Sequence conflicti83 – 831I → V in AAA35169. 1 Publication
Sequence conflicti114 – 1141S → R in CAA38402. 1 Publication
Sequence conflicti143 – 1431V → S1 Publication
Sequence conflicti146 – 1461Missing1 Publication
Sequence conflicti168 – 1681K → E in CAA36550. 1 Publication
Sequence conflicti168 – 1681K → E in AAA35169. 1 Publication
Sequence conflicti197 – 1971D → E in AAA34848. 1 Publication
Sequence conflicti215 – 2151V → R AA sequence 1 Publication
Sequence conflicti226 – 2261A → V in CAA36550. 1 Publication
Sequence conflicti226 – 2261A → V in AAA35169. 1 Publication
Sequence conflicti333 – 3331E → S AA sequence 1 Publication
Sequence conflicti351 – 3511S → P in AAA34848. 1 Publication
Sequence conflicti455 – 4551L → F in AAA34848. 1 Publication
Sequence conflicti458 – 4581G → S in CAA36550. 1 Publication
Sequence conflicti458 – 4581G → S in AAA35169. 1 Publication
Sequence conflicti505 – 5051A → AEADAEAEA1 Publication
Sequence conflicti505 – 5051A → AEADAEAEA1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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:
PDBe
RCSB PDB
PDBj
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 ENSGT00740000115037.
HOGENOMi HOG000162459.
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: September 3, 2014
This is version 148 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

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