P40087 (DDI1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA damage-inducible protein 1

Alternative name(s):
v-SNARE-master 1

Gene names

Name:	DDI1
Synonyms:	VSM1
Ordered Locus Names:	YER143W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	428 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as a linker between the 19S proteasome and polyubiquitinated proteins like the HO endonuclease and UFO1 via UBA domain interactions with ubiquitin for their subsequent degradation. Required for S-phase checkpoint control. Appears to act as negative regulator of constitutive exocytosis. May act at the level of secretory vesicle docking and fusion as a competitive inhibitor of SNARE assembly. Ref.2 Ref.8 Ref.10 Ref.11 Ref.16 Ref.17 Ref.18
Subunit structure	Forms homodimers. Interacts with RAD23. These interactions are mediated by the UBA domain. Is also able to bind ubiquitin and polyubiquitinated proteins. Interacts with the SNAREs SNC1, SNC2, SSO1, TLG1 and TLG2. Binding to SSO1 is promoted by the phosphorylation of 'Ser-49' of SSO1 by TKP1. Ref.2 Ref.7 Ref.11 Ref.16 Ref.17 Ref.18 Ref.21
Subcellular location	Cytoplasm. Cell membrane; Peripheral membrane protein; Cytoplasmic side Ref.2.
Induction	By DNA damage via PDR3. Ref.1 Ref.6 Ref.9 Ref.15
Miscellaneous	Present with 6510 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the DDI1 family. Contains 1 UBA domain. Contains 1 ubiquitin-like domain.

Ontologies

Keywords
Biological process	Protein transport Transport
Cellular component	Cell membrane Cytoplasm Membrane
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein secretion Inferred from mutant phenotype PubMed 21094643. Source: SGD ubiquitin-dependent protein catabolic process Inferred from mutant phenotype Ref.10. Source: SGD vesicle-mediated transport Inferred from mutant phenotype Ref.2. Source: SGD
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from direct assay Ref.2. Source: SGD
Molecular_function	SNARE binding Inferred from direct assay Ref.2. Source: SGD aspartic-type endopeptidase activity Inferred from sequence alignment PubMed 11516960. Source: SGD ubiquitin binding Inferred from direct assay PubMed 11323716. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 428

428

DNA damage-inducible protein 1

PRO_0000210997

Regions

Domain

1 – 80

80

Ubiquitin-like

Domain

389 – 428

40

UBA

Amino acid modifications

Modified residue

346

1

Phosphothreonine Ref.13 Ref.19 Ref.20

Modified residue

348

1

Phosphothreonine Ref.20

Cross-link

171

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.13

Cross-link

257

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.14

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

428

Helix Strand Turn

Details...

Beta strand

205 – 210

6

Beta strand

213 – 219

7

Beta strand

227 – 229

3

Helix

230 – 235

6

Helix

238 – 241

4

Beta strand

260 – 269

10

Beta strand

272 – 281

10

Beta strand

286 – 289

4

Helix

291 – 296

6

Beta strand

300 – 302

3

Turn

303 – 306

4

Beta strand

307 – 310

4

Beta strand

313 – 316

4

Turn

320 – 322

3

Sequences

	Sequence		Length	Mass (Da)
	P40087 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: B43425B029B7658B	FASTA	428	47,354
	10 20 30 40 50 60 MDLTISNELT GEIYGPIEVS EDMALTDLIA LLQADCGFDK TKHDLYYNMD ILDSNRTQSL 70 80 90 100 110 120 KELGLKTDDL LLIRGKISNS IQTDAATLSD EAFIEQFRQE LLNNQMLRSQ LILQIPGLND 130 140 150 160 170 180 LVNDPLLFRE RLGPLILQRR YGGYNTAMNP FGIPQDEYTR LMANPDDPDN KKRIAELLDQ 190 200 210 220 230 240 QAIDEQLRNA IEYTPEMFTQ VPMLYINIEI NNYPVKAFVD TGAQTTIMST RLAKKTGLSR 250 260 270 280 290 300 MIDKRFIGEA RGVGTGKIIG RIHQAQVKIE TQYIPCSFTV LDTDIDVLIG LDMLKRHLAC 310 320 330 340 350 360 VDLKENVLRI AEVETSFLSE AEIPKSFQEG LPAPTSVTTS SDKPLTPTKT SSTLPPQPGA 370 380 390 400 410 420 VPALAPRTGM GPTPTGRSTA GATTATGRTF PEQTIKQLMD LGFPRDAVVK ALKQTNGNAE FAASLLFQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Bidirectional regulation of two DNA-damage-inducible genes, MAG1 and DDI1, from Saccharomyces cerevisiae." Liu Y., Xiao W. Mol. Microbiol. 23:777-789(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION. Strain: ATCC 64665 / S288c / DC5.
[2]	"Yeast VSM1 encodes a v-SNARE binding protein that may act as a negative regulator of constitutive exocytosis." Lustgarten V., Gerst J.E. Mol. Cell. Biol. 19:4480-4494(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INTERACTION WITH SNC1 AND SNC2, SUBCELLULAR LOCATION.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"Differential regulation of two closely clustered yeast genes, MAG1 and DDI1, by cell-cycle checkpoints." Zhu Y., Xiao W. Nucleic Acids Res. 26:5402-5408(1998) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[7]	"UBA domains mediate protein-protein interactions between two DNA damage-inducible proteins." Bertolaet B.L., Clarke D.J., Wolff M., Watson M.H., Henze M., Divita G., Reed S.I. J. Mol. Biol. 313:955-963(2001) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, INTERACTION WITH RAD23.
[8]	"Dosage suppressors of pds1 implicate ubiquitin-associated domains in checkpoint control." Clarke D.J., Mondesert G., Segal M., Bertolaet B.L., Jensen S., Wolff M., Henze M., Reed S.I. Mol. Cell. Biol. 21:1997-2007(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Two alternative cell cycle checkpoint pathways differentially control DNA damage-dependent induction of MAG1 and DDI1 expression in yeast." Zhu Y., Xiao W. Mol. Genet. Genomics 266:436-444(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[10]	"Ubiquitin-like proteins and Rpn10 play cooperative roles in ubiquitin-dependent proteolysis." Saeki Y., Saitoh A., Toh-e A., Yokosawa H. Biochem. Biophys. Res. Commun. 293:986-992(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"Phosphorylation of the autoinhibitory domain of the Sso t-SNAREs promotes binding of the Vsm1 SNARE regulator in yeast." Marash M., Gerst J.E. Mol. Biol. Cell 14:3114-3125(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH SNC1; SNC2; SSO; TLG1 AND TLG2.
[12]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[13]	"A proteomics approach to understanding protein ubiquitination." Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-346, UBIQUITINATION AT LYS-171, MASS SPECTROMETRY. Strain: SUB592.
[14]	"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery." Hitchcock A.L., Auld K., Gygi S.P., Silver P.A. Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-257, MASS SPECTROMETRY.
[15]	"Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element." Zhu Y., Xiao W. Nucleic Acids Res. 32:5066-5075(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[16]	"The DNA damage-inducible UbL-UbA protein Ddi1 participates in Mec1-mediated degradation of Ho endonuclease." Kaplun L., Tzirkin R., Bakhrat A., Shabek N., Ivantsiv Y., Raveh D. Mol. Cell. Biol. 25:5355-5362(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH THE HO ENDONUCLEASE.
[17]	"Yeast UBL-UBA proteins have partially redundant functions in cell cycle control." Diaz-Martinez L.A., Kang Y., Walters K.J., Clarke D.J. Cell Div. 1:28-28(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT.
[18]	"Unique role for the UbL-UbA protein Ddi1 in turnover of SCFUfo1 complexes." Ivantsiv Y., Kaplun L., Tzirkin-Goldin R., Shabek N., Raveh D. Mol. Cell. Biol. 26:1579-1588(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH UFO1.
[19]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-346, MASS SPECTROMETRY.
[20]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-346 AND THR-348, MASS SPECTROMETRY.
[21]	"Ddi1, a eukaryotic protein with the retroviral protease fold." Sirkis R., Gerst J.E., Fass D. J. Mol. Biol. 364:376-387(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 180-325, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U14002 Genomic DNA. Translation: AAB82066.1.
AF034895 Genomic DNA. Translation: AAC18522.1.
U18917 Genomic DNA. Translation: AAB64670.1.
AY692945 Genomic DNA. Translation: AAT92964.1.
BK006939 Genomic DNA. Translation: DAA07804.1.

PIR

S50646.

RefSeq

NP_011070.3. NM_001179033.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2I1A	X-ray	2.30	A/B/C/D	180-325	[»]

ProteinModelPortal

P40087.

SMR

P40087. Positions 201-323.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1216N.

IntAct

P40087. 4 interactions.

MINT

MINT-397186.

STRING

4932.YER143W.

Protein family/group databases

MEROPS

A28.001.

Proteomic databases

PaxDb

P40087.

PeptideAtlas

P40087.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YER143W; YER143W; YER143W.

GeneID

856886.

KEGG

sce:YER143W.
sce:YER147C.

Organism-specific databases

CYGD

YER143w.

SGD

S000000945. DDI1.

Phylogenomic databases

eggNOG

NOG276681.

GeneTree

ENSGT00510000047125.

HOGENOM

HOG000234736.

KO

K06673.
K11885.

OMA

AWEISPE.

OrthoDB

EOG41RT3X.

Gene expression databases

Genevestigator

P40087.

GermOnline

YER143W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

2.40.70.10. 1 hit.

InterPro

IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic.
IPR019103. Peptidase_aspartic_DDI1-type.
IPR009060. UBA-like.
IPR000449. UBA/transl_elong_EF1B_N.
IPR015940. UBA/transl_elong_EF1B_N_euk.
[Graphical view]

Pfam

PF09668. Asp_protease. 1 hit.
PF00627. UBA. 1 hit.
[Graphical view]

SMART

SM00165. UBA. 1 hit.
[Graphical view]

SUPFAM

SSF50630. Pept_Aspartic. 1 hit.
SSF46934. UBA_like. 1 hit.

PROSITE

PS50030. UBA. 1 hit.
PS50053. UBIQUITIN_2. False negative.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P40087.

NextBio

983281.

Entry information

Entry name

DDI1_YEAST

Accession

Primary (citable) accession number: P40087
Secondary accession number(s): D3DM50

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 122 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program