Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Protein disulfide-isomerase

Gene

PDI1

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

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)DescriptionActionsGraphical viewLength
Active sitei61NucleophileBy similarity1
Sitei62Contributes to redox potential valueBy similarity1
Sitei63Contributes to redox potential valueBy similarity1
Active sitei64NucleophileBy similarity1
Sitei126Lowers pKa of C-terminal Cys of first active siteBy similarity1
Active sitei406NucleophileBy similarity1
Sitei407Contributes to redox potential valueBy similarity1
Sitei408Contributes to redox potential valueBy similarity1
Active sitei409NucleophileBy similarity1
Sitei471Lowers pKa of C-terminal Cys of second active siteBy similarity1

GO - Molecular functioni

  • protein disulfide isomerase activity Source: SGD
  • protein disulfide oxidoreductase activity Source: SGD
  • unfolded protein binding Source: SGD

GO - Biological processi

  • cell redox homeostasis Source: InterPro
  • mannose trimming involved in glycoprotein ERAD pathway Source: SGD
  • protein alpha-1,2-demannosylation Source: SGD
  • protein folding Source: SGD
  • response to endoplasmic reticulum stress Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Enzyme and pathway databases

BioCyciYEAST:YCL043C-MONOMER.
BRENDAi5.3.4.1. 984.
ReactomeiR-SCE-114608. Platelet degranulation.
R-SCE-3299685. Detoxification of Reactive Oxygen Species.
R-SCE-6798695. Neutrophil degranulation.
R-SCE-901042. Calnexin/calreticulin cycle.

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
Proteomesi
  • UP000002311 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:YCL043C.
SGDiS000000548. PDI1.

Subcellular locationi

  • Endoplasmic reticulum lumen PROSITE-ProRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Endoplasmic reticulum

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 28Or 22Sequence analysisAdd BLAST28
ChainiPRO_000003421829 – 522Protein disulfide-isomeraseAdd BLAST494

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi61 ↔ 64Redox-activePROSITE-ProRule annotation1 Publication
Glycosylationi82N-linked (GlcNAc...)Sequence analysis1
Glycosylationi117N-linked (GlcNAc...)Sequence analysis1
Glycosylationi155N-linked (GlcNAc...)Sequence analysis1
Glycosylationi174N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi406 ↔ 409Redox-activePROSITE-ProRule annotation1 Publication
Glycosylationi425N-linked (GlcNAc...)Sequence analysis1

Post-translational modificationi

The N-terminus is blocked.

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiP17967.
PRIDEiP17967.

Interactioni

Subunit structurei

Interacts with EPS1, KAR2 and MNL1.3 Publications

Binary interactionsi

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

GO - Molecular functioni

  • unfolded protein binding Source: SGD

Protein-protein interaction databases

BioGridi30941. 166 interactors.
DIPiDIP-4978N.
IntActiP17967. 10 interactors.
MINTiMINT-497035.

Structurei

Secondary structure

1522
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni39 – 41Combined sources3
Helixi42 – 46Combined sources5
Beta strandi50 – 57Combined sources8
Helixi62 – 77Combined sources16
Turni78 – 82Combined sources5
Beta strandi84 – 89Combined sources6
Turni90 – 92Combined sources3
Helixi94 – 99Combined sources6
Beta strandi104 – 112Combined sources9
Beta strandi119 – 121Combined sources3
Helixi128 – 138Combined sources11
Beta strandi142 – 145Combined sources4
Helixi149 – 155Combined sources7
Beta strandi162 – 168Combined sources7
Helixi171 – 183Combined sources13
Turni184 – 187Combined sources4
Beta strandi189 – 194Combined sources6
Beta strandi201 – 206Combined sources6
Beta strandi209 – 215Combined sources7
Helixi220 – 223Combined sources4
Helixi226 – 236Combined sources11
Helixi246 – 254Combined sources9
Beta strandi259 – 266Combined sources8
Helixi267 – 283Combined sources17
Turni284 – 287Combined sources4
Beta strandi289 – 294Combined sources6
Helixi295 – 298Combined sources4
Helixi301 – 304Combined sources4
Beta strandi311 – 318Combined sources8
Turni319 – 322Combined sources4
Beta strandi323 – 326Combined sources4
Helixi332 – 336Combined sources5
Helixi346 – 358Combined sources13
Beta strandi377 – 381Combined sources5
Turni383 – 385Combined sources3
Helixi386 – 391Combined sources6
Beta strandi397 – 402Combined sources6
Helixi407 – 426Combined sources20
Beta strandi431 – 436Combined sources6
Helixi437 – 439Combined sources3
Beta strandi448 – 456Combined sources9
Helixi473 – 483Combined sources11
Helixi490 – 501Combined sources12

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP17967.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 141Thioredoxin 1PROSITE-ProRule annotationAdd BLAST113
Domaini356 – 485Thioredoxin 2PROSITE-ProRule annotationAdd BLAST130

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi519 – 522Prevents secretion from ER4

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

GeneTreeiENSGT00860000133691.
HOGENOMiHOG000162459.
InParanoidiP17967.
KOiK09580.
OMAiLYANDED.
OrthoDBiEOG092C3SRA.

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)DescriptionActionsGraphical viewLength
Sequence conflicti33 – 52AVVKL…SHDLV → LSLSWPPTLSMNTFSRTTWW in AAA34848 (PubMed:1840696).CuratedAdd BLAST20
Sequence conflicti83I → V in CAA36550 (PubMed:1761554).Curated1
Sequence conflicti83I → V in AAA35169 (PubMed:1761554).Curated1
Sequence conflicti114S → R in CAA38402 (PubMed:1761235).Curated1
Sequence conflicti143V → S (PubMed:1761554).Curated1
Sequence conflicti146Missing (PubMed:1761554).Curated1
Sequence conflicti168K → E in CAA36550 (PubMed:1761554).Curated1
Sequence conflicti168K → E in AAA35169 (PubMed:1761554).Curated1
Sequence conflicti197D → E in AAA34848 (PubMed:1840696).Curated1
Sequence conflicti215V → R AA sequence (PubMed:1761527).Curated1
Sequence conflicti226A → V in CAA36550 (PubMed:1761554).Curated1
Sequence conflicti226A → V in AAA35169 (PubMed:1761554).Curated1
Sequence conflicti333E → S AA sequence (PubMed:1761527).Curated1
Sequence conflicti351S → P in AAA34848 (PubMed:1840696).Curated1
Sequence conflicti455L → F in AAA34848 (PubMed:1840696).Curated1
Sequence conflicti458G → S in CAA36550 (PubMed:1761554).Curated1
Sequence conflicti458G → S in AAA35169 (PubMed:1761554).Curated1
Sequence conflicti505A → AEADAEAEA (PubMed:1761554).Curated1
Sequence conflicti505A → AEADAEAEA (PubMed:1761235).Curated1

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

EnsemblFungiiCAA42373; CAA42373; CAA42373.
YCL043C; 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.
PIRiJX0182. ISBYSS.
RefSeqiNP_009887.1. NM_001178688.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi30941. 166 interactors.
DIPiDIP-4978N.
IntActiP17967. 10 interactors.
MINTiMINT-497035.

Proteomic databases

MaxQBiP17967.
PRIDEiP17967.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAA42373; CAA42373; CAA42373.
YCL043C; YCL043C; YCL043C.
GeneIDi850314.
KEGGisce:YCL043C.

Organism-specific databases

EuPathDBiFungiDB:YCL043C.
SGDiS000000548. PDI1.

Phylogenomic databases

GeneTreeiENSGT00860000133691.
HOGENOMiHOG000162459.
InParanoidiP17967.
KOiK09580.
OMAiLYANDED.
OrthoDBiEOG092C3SRA.

Enzyme and pathway databases

BioCyciYEAST:YCL043C-MONOMER.
BRENDAi5.3.4.1. 984.
ReactomeiR-SCE-114608. Platelet degranulation.
R-SCE-3299685. Detoxification of Reactive Oxygen Species.
R-SCE-6798695. Neutrophil degranulation.
R-SCE-901042. Calnexin/calreticulin cycle.

Miscellaneous databases

EvolutionaryTraceiP17967.
PROiP17967.

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]
ProtoNetiSearch...

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 30, 2016
This is version 169 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

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.