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Protein

Protein disulfide-isomerase 2

Gene

pdi-2

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in cuticle formation (PubMed:10805750). May play a role in the unfolded protein response (PubMed:21199936).2 Publications

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei52 – 521NucleophileBy similarity
Sitei53 – 531Contributes to redox potential valueBy similarity
Sitei54 – 541Contributes to redox potential valueBy similarity
Active sitei55 – 551NucleophileBy similarity
Sitei116 – 1161Lowers pKa of C-terminal Cys of first active siteBy similarity
Active sitei393 – 3931NucleophileBy similarity
Sitei394 – 3941Contributes to redox potential valueBy similarity
Sitei395 – 3951Contributes to redox potential valueBy similarity
Active sitei396 – 3961NucleophileBy similarity
Sitei456 – 4561Lowers pKa of C-terminal Cys of second active siteBy similarity

GO - Molecular functioni

  • protein disulfide isomerase activity Source: WormBase
  • protein-glutamine gamma-glutamyltransferase activity Source: WormBase

GO - Biological processi

  • cell redox homeostasis Source: InterPro
  • endoplasmic reticulum unfolded protein response Source: WormBase
  • macromolecule modification Source: WormBase
  • oxidation-reduction process Source: WormBase
  • peptidyl-proline hydroxylation to 4-hydroxy-L-proline Source: WormBase
  • protein deglutathionylation Source: WormBase
  • regulation of oxidative stress-induced intrinsic apoptotic signaling pathway Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Enzyme and pathway databases

ReactomeiR-CEL-1650814. Collagen biosynthesis and modifying enzymes.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein disulfide-isomerase 2 (EC:5.3.4.1)
Alternative name(s):
PDI 1
Prolyl 4-hydroxylase subunit beta-2
Gene namesi
Name:pdi-2
ORF Names:C07A12.4
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome X

Organism-specific databases

WormBaseiC07A12.4a; CE03972; WBGene00003963; pdi-2.

Subcellular locationi

GO - Cellular componenti

  • endoplasmic reticulum Source: WormBase
  • endoplasmic reticulum lumen Source: UniProtKB-SubCell
  • procollagen-proline 4-dioxygenase complex Source: WormBase
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum

Pathology & Biotechi

Disruption phenotypei

RNAi-mediated knockdown causes embryonic lethality characterized by a retraction of the fully elongated embryo, a progressive disorganization of the embryo and a failure to hatch (PubMed:10805750). Also causes increased expression of the unfolded protein response (UPR) marker hsp-4 (PubMed:21199936).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1616Sequence analysisAdd
BLAST
Chaini17 – 493477Protein disulfide-isomerase 2PRO_0000034204Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi52 ↔ 55Redox-activePROSITE-ProRule annotation
Glycosylationi334 – 3341N-linked (GlcNAc...)1 Publication
Disulfide bondi393 ↔ 396Redox-activePROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ17770.
PaxDbiQ17770.
PRIDEiQ17770.

PTM databases

iPTMnetiQ17770.

Expressioni

Developmental stagei

Expressed in oscillating waves in hypodermal cells during the 4 larval stages and in adults.1 Publication

Gene expression databases

ExpressionAtlasiQ17770. baseline and differential.

Interactioni

Subunit structurei

Heterotetramer of two alpha chains and two beta chains. Exist either as a phy-12/pdi-22 tetramer, a phy-22/pdi-22 tetramer or as a phy-1/phy-2/pdi-22 tetramer.1 Publication

Protein-protein interaction databases

BioGridi45659. 8 interactions.
IntActiQ17770. 5 interactions.
MINTiMINT-230414.
STRINGi6239.C07A12.4a.1.

Structurei

3D structure databases

ProteinModelPortaliQ17770.
SMRiQ17770. Positions 6-473.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini17 – 130114Thioredoxin 1PROSITE-ProRule annotationAdd
BLAST
Domaini342 – 470129Thioredoxin 2PROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi490 – 4934Prevents secretion from ERSequence analysis

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

eggNOGiKOG0190. Eukaryota.
COG0526. LUCA.
GeneTreeiENSGT00760000119201.
HOGENOMiHOG000162459.
InParanoidiQ17770.
KOiK09580.
OMAiSKFTQNY.
PhylomeDBiQ17770.

Family and domain databases

Gene3Di3.40.30.10. 4 hits.
InterProiIPR005788. Disulphide_isomerase.
IPR005792. 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.
TIGR01126. pdi_dom. 2 hits.
PROSITEiPS00194. 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.

Q17770-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFRLVGLFFL VLGASAAVIE EEENVIVLTK DNFDEVINGN EFILVEFYAP
60 70 80 90 100
WCGHCKSLAP EYAKAATQLK EEGSDIKLGK LDATVHGEVS SKFEVRGYPT
110 120 130 140 150
LKLFRNGKPQ EYNGGRDHDS IIAWLKKKTG PVAKPLADAD AVKELQESAD
160 170 180 190 200
VVVIGYFKDT TSDDAKTFLE VAAGIDDVPF GISTEDAVKS EIELKGEGIV
210 220 230 240 250
LFKKFDDGRV AFDEKLTQDG LKTWIQANRL ALVSEFTQET ASVIFGGEIK
260 270 280 290 300
SHNLLFVSKE SSEFAKLEQE FKNAAKQFKG KVLFVYINTD VEENARIMEF
310 320 330 340 350
FGLKKDELPA IRLISLEEDM TKFKPDFEEI TTENISKFTQ NYLDGSVKPH
360 370 380 390 400
LMSEDIPEDW DKNPVKILVG KNFEQVARDN TKNVLVEFYA PWCGHCKQLA
410 420 430 440 450
PTWDKLGEKF ADDESIVIAK MDSTLNEVED VKIQSFPTIK FFPAGSNKVV
460 470 480 490
DYTGDRTIEG FTKFLETNGK EGAGASEEEK AEEEADEEGH TEL
Length:493
Mass (Da):55,152
Last modified:November 1, 1996 - v1
Checksum:i41BC0C1185EBFB5E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO080373 Genomic DNA. Translation: CCD63277.1.
PIRiS71862.
T34092.
RefSeqiNP_508778.1. NM_076377.3.
UniGeneiCel.18353.

Genome annotation databases

EnsemblMetazoaiC07A12.4a.1; C07A12.4a.1; WBGene00003963.
C07A12.4a.2; C07A12.4a.2; WBGene00003963.
GeneIDi180724.
KEGGicel:CELE_C07A12.4.
UCSCiC07A12.4a.1. c. elegans.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO080373 Genomic DNA. Translation: CCD63277.1.
PIRiS71862.
T34092.
RefSeqiNP_508778.1. NM_076377.3.
UniGeneiCel.18353.

3D structure databases

ProteinModelPortaliQ17770.
SMRiQ17770. Positions 6-473.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi45659. 8 interactions.
IntActiQ17770. 5 interactions.
MINTiMINT-230414.
STRINGi6239.C07A12.4a.1.

PTM databases

iPTMnetiQ17770.

Proteomic databases

EPDiQ17770.
PaxDbiQ17770.
PRIDEiQ17770.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiC07A12.4a.1; C07A12.4a.1; WBGene00003963.
C07A12.4a.2; C07A12.4a.2; WBGene00003963.
GeneIDi180724.
KEGGicel:CELE_C07A12.4.
UCSCiC07A12.4a.1. c. elegans.

Organism-specific databases

CTDi180724.
WormBaseiC07A12.4a; CE03972; WBGene00003963; pdi-2.

Phylogenomic databases

eggNOGiKOG0190. Eukaryota.
COG0526. LUCA.
GeneTreeiENSGT00760000119201.
HOGENOMiHOG000162459.
InParanoidiQ17770.
KOiK09580.
OMAiSKFTQNY.
PhylomeDBiQ17770.

Enzyme and pathway databases

ReactomeiR-CEL-1650814. Collagen biosynthesis and modifying enzymes.

Miscellaneous databases

PROiQ17770.

Gene expression databases

ExpressionAtlasiQ17770. baseline and differential.

Family and domain databases

Gene3Di3.40.30.10. 4 hits.
InterProiIPR005788. Disulphide_isomerase.
IPR005792. 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.
TIGR01126. pdi_dom. 2 hits.
PROSITEiPS00194. THIOREDOXIN_1. 2 hits.
PS51352. THIOREDOXIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Baculovirus expression of two protein disulphide isomerase isoforms from Caenorhabditis elegans and characterization of prolyl 4-hydroxylases containing one of these polypeptides as their beta subunit."
    Veijola J., Annunen P., Koivunen P., Page A.P., Pihlajaniemi T., Kivirikko K.I.
    Biochem. J. 317:721-729(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.
  3. "Prolyl 4-hydroxylase is an essential procollagen-modifying enzyme required for exoskeleton formation and the maintenance of body shape in the nematode Caenorhabditis elegans."
    Winter A.D., Page A.P.
    Mol. Cell. Biol. 20:4084-4093(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
  4. "The exoskeleton collagens in Caenorhabditis elegans are modified by prolyl 4-hydroxylases with unique combinations of subunits."
    Myllyharju J., Kukkola L., Winter A.D., Page A.P.
    J. Biol. Chem. 277:29187-29196(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  5. "Proteomics reveals N-linked glycoprotein diversity in Caenorhabditis elegans and suggests an atypical translocation mechanism for integral membrane proteins."
    Kaji H., Kamiie J., Kawakami H., Kido K., Yamauchi Y., Shinkawa T., Taoka M., Takahashi N., Isobe T.
    Mol. Cell. Proteomics 6:2100-2109(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-334, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Bristol N2.
  6. "Selenoprotein TRXR-1 and GSR-1 are essential for removal of old cuticle during molting in Caenorhabditis elegans."
    Stenvall J., Fierro-Gonzalez J.C., Swoboda P., Saamarthy K., Cheng Q., Cacho-Valadez B., Arner E.S., Persson O.P., Miranda-Vizuete A., Tuck S.
    Proc. Natl. Acad. Sci. U.S.A. 108:1064-1069(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiPDI2_CAEEL
AccessioniPrimary (citable) accession number: Q17770
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2003
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 142 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

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.