Q8VX13 (PDI13_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein disulfide isomerase-like 1-3
Short name=AtPDIL1-3
EC=5.3.4.1

Alternative name(s):
Protein disulfide isomerase 1
Short name=AtPDI1
Protein disulfide isomerase-like 2-1
Short name=AtPDIL2-1

Gene names

Name:	PDIL1-3
Synonyms:	PDI1, PDI72, PDIL2-1
Ordered Locus Names:	At3g54960
ORF Names:	F28P10.60, T15C9.4

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	579 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Acts as a protein-folding catalyst that interacts with nascent polypeptides to catalyze the formation, isomerization, and reduction or oxidation of disulfide bonds By similarity.
Catalytic activity	Catalyzes the rearrangement of -S-S- bonds in proteins.
Subcellular location	Endoplasmic reticulum lumen Probable.
Tissue specificity	Widely expressed. Ref.7
Induction	By chemically-induced ER stress response. Ref.7
Sequence similarities	Belongs to the protein disulfide isomerase family. Contains 2 thioredoxin domains.
Sequence caution	The sequence CAB41088.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Cellular component	Endoplasmic reticulum
Coding sequence diversity	Alternative splicing
Domain	Redox-active center Repeat Signal
Molecular function	Isomerase
PTM	Disulfide bond Glycoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell redox homeostasis Inferred from electronic annotation. Source: InterPro response to endoplasmic reticulum stress Inferred from expression pattern Ref.7. Source: TAIR
Cellular_component	chloroplast Inferred from direct assay PubMed 15028209. Source: TAIR endoplasmic reticulum Inferred from direct assay PubMed 16618929PubMed 22923678. Source: TAIR endoplasmic reticulum lumen Inferred from electronic annotation. Source: UniProtKB-SubCell vacuolar membrane Inferred from direct assay PubMed 17151019. Source: TAIR
Molecular_function	protein disulfide isomerase activity Inferred from sequence or structural similarity Ref.7. Source: TAIR
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q8VX13-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q8VX13-2)

The sequence of this isoform differs from the canonical sequence as follows:
     507-518: ADGFPTILFFPG → VIKKKELRKSFW
     519-579: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 25	25	Potential
	Chain	26 – 579	554	Protein disulfide isomerase-like 1-3		PRO_5000065917
Regions
	Domain	81 – 204	124	Thioredoxin 1
	Domain	416 – 546	131	Thioredoxin 2
	Motif	576 – 579	4	Prevents secretion from ER By similarity
Sites
	Active site	128	1	Nucleophile By similarity
	Active site	131	1	Nucleophile By similarity
	Active site	467	1	Nucleophile By similarity
	Active site	470	1	Nucleophile By similarity
	Site	190	1	Lowers pKa of C-terminal Cys of first active site By similarity
	Site	468	1	Contributes to redox potential value By similarity
	Site	469	1	Contributes to redox potential value By similarity
	Site	532	1	Lowers pKa of C-terminal Cys of second active site By similarity
Amino acid modifications
	Glycosylation	27	1	N-linked (GlcNAc...) Potential
	Glycosylation	108	1	N-linked (GlcNAc...) Potential
	Glycosylation	115	1	N-linked (GlcNAc...) Potential
	Glycosylation	209	1	N-linked (GlcNAc...) Potential
	Glycosylation	293	1	N-linked (GlcNAc...) Potential
	Glycosylation	313	1	N-linked (GlcNAc...) Potential
	Glycosylation	338	1	N-linked (GlcNAc...) Potential
	Glycosylation	520	1	N-linked (GlcNAc...) Potential
	Disulfide bond	128 ↔ 131		Redox-active By similarity
	Disulfide bond	467 ↔ 470		Redox-active By similarity
Natural variations
	Alternative sequence	507 – 518	12	ADGFP…LFFPG → VIKKKELRKSFW in isoform 2.		VSP_039979
	Alternative sequence	519 – 579	61	Missing in isoform 2.		VSP_039980

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified March 1, 2002. Version 1. Checksum: 0DF50E500B24B829	FASTA	579	64,212
	10 20 30 40 50 60 MASSSTSISL LLFVSFILLL VNSRAENASS GSDLDEELAF LAAEESKEQS HGGGSYHEEE 70 80 90 100 110 120 HDHQHRDFEN YDDLEQGGGE FHHGDHGYEE EPLPPVDEKD VAVLTKDNFT EFVGNNSFAM 130 140 150 160 170 180 VEFYAPWCGA CQALTPEYAA AATELKGLAA LAKIDATEEG DLAQKYEIQG FPTVFLFVDG 190 200 210 220 230 240 EMRKTYEGER TKDGIVTWLK KKASPSIHNI TTKEEAERVL SAEPKLVFGF LNSLVGSESE 250 260 270 280 290 300 ELAAASRLED DLSFYQTASP DIAKLFEIET QVKRPALVLL KKEEEKLARF DGNFTKTAIA 310 320 330 340 350 360 EFVSANKVPL VINFTREGAS LIFESSVKNQ LILFAKANES EKHLPTLREV AKSFKGKFVF 370 380 390 400 410 420 VYVQMDNEDY GEAVSGFFGV TGAAPKVLVY TGNEDMRKFI LDGELTVNNI KTLAEDFLAD 430 440 450 460 470 480 KLKPFYKSDP LPENNDGDVK VIVGNNFDEI VLDESKDVLL EIYAPWCGHC QSFEPIYNKL 490 500 510 520 530 540 GKYLKGIDSL VVAKMDGTSN EHPRAKADGF PTILFFPGGN KSFDPIAVDV DRTVVELYKF 550 560 570 LKKHASIPFK LEKPATPEPV ISTMKSDEKI EGDSSKDEL
	Isoform 2 [UniParc]. Checksum: B3AA1BB3BAFE49FF	FASTA	518	57,691
	10 20 30 40 50 60 MASSSTSISL LLFVSFILLL VNSRAENASS GSDLDEELAF LAAEESKEQS HGGGSYHEEE 70 80 90 100 110 120 HDHQHRDFEN YDDLEQGGGE FHHGDHGYEE EPLPPVDEKD VAVLTKDNFT EFVGNNSFAM 130 140 150 160 170 180 VEFYAPWCGA CQALTPEYAA AATELKGLAA LAKIDATEEG DLAQKYEIQG FPTVFLFVDG 190 200 210 220 230 240 EMRKTYEGER TKDGIVTWLK KKASPSIHNI TTKEEAERVL SAEPKLVFGF LNSLVGSESE 250 260 270 280 290 300 ELAAASRLED DLSFYQTASP DIAKLFEIET QVKRPALVLL KKEEEKLARF DGNFTKTAIA 310 320 330 340 350 360 EFVSANKVPL VINFTREGAS LIFESSVKNQ LILFAKANES EKHLPTLREV AKSFKGKFVF 370 380 390 400 410 420 VYVQMDNEDY GEAVSGFFGV TGAAPKVLVY TGNEDMRKFI LDGELTVNNI KTLAEDFLAD 430 440 450 460 470 480 KLKPFYKSDP LPENNDGDVK VIVGNNFDEI VLDESKDVLL EIYAPWCGHC QSFEPIYNKL 490 500 510 GKYLKGIDSL VVAKMDGTSN EHPRAKVIKK KELRKSFW

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Arabidopsis thaliana mRNA for ERp72." Mahon P. Thesis (2000), Cambridge University, United Kingdom Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]	"Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana." Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F. , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S. Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: cv. Columbia.
[5]	"Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs." Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K. DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: cv. Columbia.
[6]	"Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins." Houston N.L., Fan C., Xiang J.Q., Schulze J.M., Jung R., Boston R.S. Plant Physiol. 137:762-778(2005) [PubMed] [Europe PMC] [Abstract] Cited for: GENE FAMILY, NOMENCLATURE.
[7]	"Endoplasmic reticulum stress activates the expression of a sub-group of protein disulfide isomerase genes and AtbZIP60 modulates the response in Arabidopsis thaliana." Lu D.-P., Christopher D.A. Mol. Genet. Genomics 280:199-210(2008) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY, INDUCTION.
[8]	"The protein disulfide isomerase gene family in bread wheat (T. aestivum L.)." d'Aloisio E., Paolacci A.R., Dhanapal A.P., Tanzarella O.A., Porceddu E., Ciaffi M. BMC Plant Biol. 10:101-101(2010) [PubMed] [Europe PMC] [Abstract] Cited for: GENE FAMILY, NOMENCLATURE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AK318844 mRNA. Translation: BAH56959.1. AJ271376 mRNA. Translation: CAC81067.1. AL049655 Genomic DNA. Translation: CAB41088.1. Sequence problems. AL132970 Genomic DNA. No translation available. CP002686 Genomic DNA. Translation: AEE79318.1. CP002686 Genomic DNA. Translation: AEE79319.1. AY093115 mRNA. Translation: AAM13114.1. BT000172 mRNA. Translation: AAN15491.1.
IPI	IPI00524564. IPI00891832.
PIR	T06724.
RefSeq	NP_001118842.1. NM_001125370.1. NP_191056.2. NM_115353.4.
UniGene	At.22358.
3D structure databases
HSSP	HSSP built from PDB template 1MEK based on UniProtKB P07237.
ProteinModelPortal	Q8VX13.
SMR	Q8VX13. Positions 100-548.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8VX13. 1 interaction.
STRING	3702.AT3G54960.1-P.
Proteomic databases
PaxDb	Q8VX13.
PRIDE	Q8VX13.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT3G54960.1; AT3G54960.1; AT3G54960.
GeneID	824661.
KEGG	ath:AT3G54960.
Organism-specific databases
TAIR	At3g54960.
Phylogenomic databases
eggNOG	COG0526.
HOGENOM	HOG000162459.
InParanoid	Q8VX13.
KO	K09580.
OMA	KSFEPIT.
PhylomeDB	Q8VX13.
ProtClustDB	CLSN2690609.
Gene expression databases
Genevestigator	Q8VX13.
Family and domain databases
Gene3D	3.40.30.10. 4 hits.
InterPro	IPR005792. Prot_disulphide_isomerase. IPR012336. Thioredoxin-like_fold. IPR017937. Thioredoxin_CS. IPR013766. Thioredoxin_domain. [Graphical view]
Pfam	PF00085. Thioredoxin. 2 hits. [Graphical view]
SUPFAM	SSF52833. Thiordxn-like_fd. 4 hits.
TIGRFAMs	TIGR01130. ER_PDI_fam. 1 hit.
PROSITE	PS00014. ER_TARGET. 1 hit. PS00194. THIOREDOXIN_1. 2 hits. PS51352. THIOREDOXIN_2. 2 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PDI13_ARATH

Accession

Primary (citable) accession number: Q8VX13
Secondary accession number(s): B3H5N9, Q9SV44

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 2, 2010
Last sequence update:	March 1, 2002
Last modified:	May 1, 2013
This is version 95 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program