Reviewed, UniProtKB/Swiss-Prot P17967 (PDI_YEAST)

Names and origin

Protein names

Recommended name:
    Protein disulfide-isomerase
      Short name=PDI
    EC=5.3.4.1
Alternative name(s):
    Thioredoxin-related glycoprotein 1

Gene names

Name:	PDI1
Synonyms:	MFP1, TRG1
Ordered Locus Names:	YCL043C
ORF Names:	YCL43C, YCL313

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	522 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Participates in the folding of proteins containing disulfide bonds, may be involved in glycosylation, prolyl hydroxylation and triglyceride transfer.
Catalytic activity	Catalyzes the rearrangement of -S-S- bonds in proteins.
Subcellular location	Endoplasmic reticulum lumen Potential.
Post-translational modification	The N-terminus is blocked.
Sequence similarities	Belongs to the protein disulfide isomerase family. Contains 2 thioredoxin domains.

Ontologies

Keywords
Cellular component	Endoplasmic reticulum
Domain	Redox-active center Repeat Signal
Molecular function	Isomerase
PTM	Disulfide bond Glycoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	cell redox homeostasis Inferred from electronic annotation. Source: InterPro protein folding Inferred from mutant phenotype. Source: SGD
Cellular component	endoplasmic reticulum lumen Ref.4 Inferred from direct assay. Source: SGD
Molecular function	protein binding Inferred from physical interaction. Source: IntAct protein disulfide isomerase activity Ref.8 Inferred from direct assay. Source: SGD protein disulfide oxidoreductase activity Inferred from direct assay. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MNL1	P38888	1	EBI-13012,EBI-24256
RNASE1	P61823	2	EBI-13012,EBI-908364	From a different organism.
RSP5	P39940	1	EBI-13012,EBI-16219
SSM4	P40318	1	EBI-13012,EBI-18208

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 28

28

Or 22 Potential

Chain

29 – 522

494

Protein disulfide-isomerase

PRO_0000034218

Regions

Domain

29 – 141

113

Thioredoxin 1

Domain

356 – 485

130

Thioredoxin 2

Motif

519 – 522

4

Prevents secretion from ER

Sites

Active site

61

1

Nucleophile By similarity

Active site

64

1

Nucleophile By similarity

Active site

406

1

Nucleophile By similarity

Active site

409

1

Nucleophile By similarity

Site

62

1

Contributes to redox potential value By similarity

Site

63

1

Contributes to redox potential value By similarity

Site

126

1

Lowers pKa of C-terminal Cys of first active site By similarity

Site

407

1

Contributes to redox potential value By similarity

Site

408

1

Contributes to redox potential value By similarity

Site

471

1

Lowers pKa of C-terminal Cys of second active site By similarity

Amino acid modifications

Glycosylation

82

1

N-linked (GlcNAc...) Potential

Glycosylation

117

1

N-linked (GlcNAc...) Potential

Glycosylation

155

1

N-linked (GlcNAc...) Potential

Glycosylation

174

1

N-linked (GlcNAc...) Potential

Glycosylation

425

1

N-linked (GlcNAc...) Potential

Disulfide bond

61 ↔ 64

Redox-active Ref.8

Disulfide bond

406 ↔ 409

Redox-active Ref.8

Experimental info

Sequence conflict

33 – 52

20

AVVKL…SHDLV → LSLSWPPTLSMNTFSRTTWW in AAA34848. Ref.3

Sequence conflict

83

1

I → V in CAA36550. Ref.4

Sequence conflict

83

1

I → V in AAA35169. Ref.4

Sequence conflict

114

1

S → R in CAA38402. Ref.5

Sequence conflict

143

1

V → S Ref.4

Sequence conflict

146

1

Missing Ref.4

Sequence conflict

168

1

K → E in CAA36550. Ref.4

Sequence conflict

168

1

K → E in AAA35169. Ref.4

Sequence conflict

197

1

D → E in AAA34848. Ref.3

Sequence conflict

215

1

V → R AA sequence Ref.1

Sequence conflict

226

1

A → V in CAA36550. Ref.4

Sequence conflict

226

1

A → V in AAA35169. Ref.4

Sequence conflict

333

1

E → S AA sequence Ref.1

Sequence conflict

351

1

S → P in AAA34848. Ref.3

Sequence conflict

455

1

L → F in AAA34848. Ref.3

Sequence conflict

458

1

G → S in CAA36550. Ref.4

Sequence conflict

458

1

G → S in AAA35169. Ref.4

Sequence conflict

505

1

A → AEADAEAEA Ref.4

Sequence conflict

505

1

A → AEADAEAEA Ref.5

Secondary structure

1

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522

Helix Strand Turn

Details...

Turn

39 – 41

3

Helix

42 – 46

5

Beta strand

50 – 57

8

Helix

62 – 77

16

Turn

78 – 82

5

Beta strand

84 – 89

6

Turn

90 – 92

3

Helix

94 – 99

6

Beta strand

104 – 112

9

Beta strand

119 – 121

3

Helix

128 – 138

11

Beta strand

142 – 145

4

Helix

149 – 155

7

Beta strand

162 – 168

7

Helix

171 – 183

13

Turn

184 – 187

4

Beta strand

189 – 194

6

Beta strand

201 – 206

6

Beta strand

209 – 215

7

Helix

220 – 223

4

Helix

226 – 236

11

Helix

246 – 254

9

Beta strand

259 – 266

8

Helix

267 – 283

17

Turn

284 – 287

4

Beta strand

289 – 294

6

Helix

295 – 298

4

Helix

301 – 304

4

Beta strand

311 – 318

8

Turn

319 – 322

4

Beta strand

323 – 326

4

Helix

332 – 336

5

Helix

346 – 358

13

Beta strand

377 – 381

5

Turn

383 – 385

3

Helix

386 – 391

6

Beta strand

397 – 402

6

Helix

407 – 426

20

Beta strand

431 – 436

6

Helix

437 – 439

3

Beta strand

448 – 456

9

Helix

473 – 483

11

Helix

490 – 501

12

Sequences

	Sequence		Length	Mass (Da)
	P17967-1 [UniParc]. Last modified March 1, 1992. Version 2. Checksum: 69CF3E05D7F74C94	FASTA	522	58,227
	10 20 30 40 50 60 MKFSAGAVLS WSSLLLASSV FAQQEAVAPE DSAVVKLATD SFNEYIQSHD LVLAEFFAPW 70 80 90 100 110 120 CGHCKNMAPE YVKAAETLVE KNITLAQIDC TENQDLCMEH NIPGFPSLKI FKNSDVNNSI 130 140 150 160 170 180 DYEGPRTAEA IVQFMIKQSQ PAVAVVADLP AYLANETFVT PVIVQSGKID ADFNATFYSM 190 200 210 220 230 240 ANKHFNDYDF VSAENADDDF KLSIYLPSAM DEPVVYNGKK ADIADADVFE KWLQVEALPY 250 260 270 280 290 300 FGEIDGSVFA QYVESGLPLG YLFYNDEEEL EEYKPLFTEL AKKNRGLMNF VSIDARKFGR 310 320 330 340 350 360 HAGNLNMKEQ FPLFAIHDMT EDLKYGLPQL SEEAFDELSD KIVLESKAIE SLVKDFLKGD 370 380 390 400 410 420 ASPIVKSQEI FENQDSSVFQ LVGKNHDEIV NDPKKDVLVL YYAPWCGHCK RLAPTYQELA 430 440 450 460 470 480 DTYANATSDV LIAKLDHTEN DVRGVVIEGY PTIVLYPGGK KSESVVYQGS RSLDSLFDFI 490 500 510 520 KENGHFDVDG KALYEEAQEK AAEEADADAE LADEEDAIHD EL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 1761527] [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: 2063627] [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: 1840696] [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: 1761554] [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: 1761235] [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: 1523890] [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: 1574125] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[8]	"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: 16413482] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 23-522, DISULFIDE BONDS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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.

PIR

ISBYSS. JX0182.

RefSeq

NP_009887.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2B5E	X-ray	2.40	A	23-522	[»]
3BOA	X-ray	3.70	A	23-522	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:4978N.

IntAct

P17967. 13 interactions.

STRING

P17967.

Proteomic databases

PeptideAtlas

P17967.

PRIDE

P17967.

Genome annotation databases

Ensembl

YCL043C; YCL043C; YCL043C; Saccharomyces cerevisiae. [Genome view]

GeneID

850314.

GenomeReviews

Gene locus YCL043C in contig X59720_GR.

KEGG

sce:YCL043C.

NMPDR

fig|4932.3.peg.607.

Organism-specific databases

CYGD

YCL043c.

SGD

S000000548. PDI1.

Phylogenomic databases

HOGENOM

P17967.

OMA

CTENEEL.

Enzyme and pathway databases

BRENDA

5.3.4.1. 250.

Gene expression databases

ArrayExpress

P17967.

Genevestigator

P17967.

GermOnline

YCL043C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005788. Disulphide_isomerase.
IPR000886. ER_target_seq_motif.
IPR005792. Prot_disulphide_isomerase.
IPR017936. Thioredoxin-like.
IPR006662. Thioredoxin-like_subdom.
IPR017937. Thioredoxin_CS.
IPR013766. Thioredoxin_domain.
IPR012335. Thioredoxin_fold.
[Graphical view]

Gene3D

G3DSA:3.40.30.10. Thioredoxin_fold. 2 hits.

Pfam

PF00085. Thioredoxin. 2 hits.
[Graphical view]

PRINTS

PR00421. THIOREDOXIN.

TIGRFAMs

TIGR01130. ER_PDI_fam. 1 hit.
TIGR01126. pdi_dom. 2 hits.

PROSITE

PS00014. ER_TARGET. 1 hit.
PS00194. THIOREDOXIN_1. 2 hits.
PS51352. THIOREDOXIN_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

965715.

Entry information

Entry name

PDI_YEAST

Accession

Primary (citable) accession number: P17967

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	March 1, 1992
Last modified:	November 3, 2009
This is version 104 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)