P36037 (DOA1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein DOA1

Gene names

Name:	DOA1
Synonyms:	UFD3, ZZZ4
Ordered Locus Names:	YKL213C

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	715 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone. May act by preventing the interaction between CDC48 and the E4 enzyme UFD2, leading to prevent multiubiquitination of substrates and subsequent degradation. Essential for maintaining cellular ubiquitin levels. Ref.5 Ref.6
Subunit structure	Interacts with CDC48, OTU1 and ubiquitin. Ref.9 Ref.10 Ref.13
Subcellular location	Nucleus. Cytoplasm Ref.7.
Domain	The PUL domain is composed of 6 armadillo-like repeats and mediates the interaction with CDC48 C-terminus. The PFU domain mediates interaction with ubiquitin.
Miscellaneous	Present with 6800 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the WD repeat PLAP family. Contains 6 ARM repeats. Contains 1 PFU domain. Contains 1 PUL domain. Contains 7 WD repeats.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cytoplasm Nucleus
Domain	Repeat WD repeat
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	double-strand break repair via nonhomologous end joining Inferred from mutant phenotype PubMed 12399380. Source: SGD ubiquitin-dependent protein catabolic process Inferred from mutant phenotype PubMed 2111732. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay Ref.7PubMed 22842922. Source: SGD nucleus Inferred from direct assay Ref.7PubMed 22842922. Source: SGD
Molecular_function	ubiquitin binding Inferred from direct assay Ref.10PubMed 21070969. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 715

715

Protein DOA1

PRO_0000050958

Regions

Repeat

11 – 40

30

WD 1

Repeat

53 – 82

30

WD 2

Repeat

97 – 125

29

WD 3

Repeat

135 – 166

32

WD 4

Repeat

177 – 206

30

WD 5

Repeat

218 – 247

30

WD 6

Repeat

259 – 288

30

WD 7

Domain

352 – 449

98

PFU

Domain

465 – 715

251

PUL

Repeat

478 – 512

35

ARM 1

Repeat

513 – 543

31

ARM 2

Repeat

544 – 582

39

ARM 3

Repeat

583 – 635

53

ARM 4

Repeat

636 – 680

45

ARM 5

Repeat

681 – 715

35

ARM 6

Amino acid modifications

Modified residue

332

1

Phosphoserine Ref.11 Ref.12

Modified residue

454

1

Phosphoserine Ref.12

Modified residue

457

1

Phosphoserine Ref.11 Ref.12

Modified residue

459

1

Phosphoserine Ref.12

Experimental info

Mutagenesis

541

1

R → A: Depletion of cellular ubiquitin pools and reduced activity of the ubiquitin fusion degradation pathway. Ref.13

Mutagenesis

669

1

R → A: Depletion of cellular ubiquitin pools and reduced activity of the ubiquitin fusion degradation pathway. Ref.13

Sequence conflict

180

1

D → DI AA sequence Ref.5

Secondary structure

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715

Helix Strand Turn

Details...

Beta strand

4 – 9

6

Beta strand

16 – 23

8

Beta strand

26 – 31

6

Beta strand

34 – 52

19

Beta strand

57 – 63

7

Turn

64 – 67

4

Beta strand

68 – 73

6

Beta strand

78 – 82

5

Beta strand

102 – 108

7

Beta strand

111 – 116

6

Beta strand

119 – 125

7

Beta strand

128 – 134

7

Beta strand

140 – 147

8

Turn

148 – 151

4

Beta strand

152 – 157

6

Beta strand

162 – 166

5

Beta strand

169 – 174

6

Beta strand

182 – 189

8

Beta strand

192 – 197

6

Beta strand

200 – 206

7

Turn

207 – 209

3

Beta strand

212 – 217

6

Beta strand

223 – 228

6

Beta strand

234 – 238

5

Beta strand

241 – 246

6

Turn

248 – 250

3

Beta strand

253 – 258

6

Beta strand

260 – 262

3

Beta strand

264 – 269

6

Beta strand

275 – 279

5

Beta strand

284 – 289

6

Helix

291 – 293

3

Beta strand

378 – 380

3

Beta strand

383 – 391

9

Beta strand

400 – 404

5

Helix

410 – 420

11

Helix

425 – 427

3

Helix

428 – 438

11

Helix

480 – 494

15

Helix

499 – 509

11

Helix

512 – 529

18

Helix

534 – 543

10

Helix

544 – 546

3

Helix

550 – 553

4

Helix

554 – 560

7

Helix

566 – 579

14

Turn

583 – 585

3

Helix

586 – 590

5

Helix

593 – 596

4

Helix

599 – 602

4

Beta strand

608 – 610

3

Helix

612 – 634

23

Helix

642 – 651

10

Turn

652 – 656

5

Helix

658 – 662

5

Helix

664 – 680

17

Helix

682 – 685

4

Turn

688 – 690

3

Helix

692 – 701

10

Helix

705 – 714

10

Sequences

	Sequence		Length	Mass (Da)
	P36037 [UniParc]. Last modified June 1, 1994. Version 1. Checksum: 593B808169283B5F	FASTA	715	79,506
	10 20 30 40 50 60 MGYQLSATLK GHDQDVRDVV AVDDSKVASV SRDGTVRLWS KDDQWLGTVV YTGQGFLNSV 70 80 90 100 110 120 CYDSEKELLL FGGKDTMING VPLFATSGED PLYTLIGHQG NVCSLSFQDG VVISGSWDKT 130 140 150 160 170 180 AKVWKEGSLV YNLQAHNASV WDAKVVSFSE NKFLTASADK TIKLWQNDKV IKTFSGIHND 190 200 210 220 230 240 VVRHLAVVDD GHFISCSNDG LIKLVDMHTG DVLRTYEGHE SFVYCIKLLP NGDIVSCGED 250 260 270 280 290 300 RTVRIWSKEN GSLKQVITLP AISIWSVDCM SNGDIIVGSS DNLVRIFSQE KSRWASEDEI 310 320 330 340 350 360 NELSTQVEKS TISSKTIEFD ESKLSPYEIL QSPGRKEGQI VVVKSPQGTI EAHQFSNSSW 370 380 390 400 410 420 KKVGDVVGAG ATGNDKKIEF EGKTYDYVFD VDIEDGKPPL KLPINVSDNP YTAADNFLAR 430 440 450 460 470 480 YELPMSYRDQ VVQFILKNTN GISLDQPNDN ASSSAVSPSK TSVMKVLPVK QYLIMENYNP 490 500 510 520 530 540 DTIFNGIVKI NSNEKTFDDE ILAQIGGALH DIDESWELLL SFANTIRSNW EIKTPAYDIV 550 560 570 580 590 600 RLIVKKLPYS SDIKDYIEEG LGNKNITLTM LTVRILVNCF NNENWGVKLL ESNQVYKSIF 610 620 630 640 650 660 ETIDTEFSQA SAKQSQNLAI AVSTLIFNYS ALVTKGNSDL ELLPIVADAI NTKYGPLEEY 670 680 690 700 710 QECEEAAYRL TVAYGNLATV EPTLRQFANS VTWLANIKRS YGNVPRFKDI FDDLS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	Hochstrasser M., Gang G. Submitted (NOV-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The complete sequencing of a 24.6 kb segment of yeast chromosome XI identified the known loci URA1, SAC1 and TRP3, and revealed 6 new open reading frames including homologues to the threonine dehydratases, membrane transporters, hydantoinases and the phospholipase A2-activating protein." Tzermia M., Horaitis O., Alexandraki D. Yeast 10:663-679(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"Complete DNA sequence of yeast chromosome XI." Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W. Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Identification of a novel 29-linked polyubiquitin binding protein, Ufd3, using polyubiquitin chain analogues." Russell N.S., Wilkinson K.D. Biochemistry 43:4844-4854(2004) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 126-144; 173-183; 215-227; 316-335; 345-361; 384-420; 534-541; 598-613; 654-685 AND 700-706, FUNCTION.
[6]	"Cdc48p interacts with Ufd3p, a WD repeat protein required for ubiquitin-mediated proteolysis in Saccharomyces cerevisiae." Ghislain M., Dohmen R.J., Levy F., Varshavsky A. EMBO J. 15:4884-4899(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[8]	"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].
[9]	"Functional division of substrate processing cofactors of the ubiquitin-selective Cdc48 chaperone." Rumpf S., Jentsch S. Mol. Cell 21:261-269(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH OTU1 AND CDC48.
[10]	"Doa1 is a Cdc48 adapter that possesses a novel ubiquitin binding domain." Mullally J.E., Chernova T., Wilkinson K.D. Mol. Cell. Biol. 26:822-830(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH UBIQUITIN AND CDC48.
[11]	"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 SER-332 AND SER-457, MASS SPECTROMETRY.
[12]	"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 SER-332; SER-454; SER-457 AND SER-459, MASS SPECTROMETRY.
[13]	"An Armadillo motif in Ufd3 interacts with Cdc48 and is involved in ubiquitin homeostasis and protein degradation." Zhao G., Li G., Schindelin H., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 106:16197-16202(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 464-715, INTERACTION WITH CDC48, ARM REPEATS, MUTAGENESIS OF ARG-541 AND ARG-669.
[14]	"Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3." Nishimasu R., Komori H., Higuchi Y., Nishimasu H., Hiroaki H. Kobe J. Med. Sci. 56:E125-E139(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 354-715, ARM REPEATS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U39947 Genomic DNA. Translation: AAA82258.1.
X75951 Genomic DNA. Translation: CAA53560.1.
Z28213 Genomic DNA. Translation: CAA82058.1.
BK006944 Genomic DNA. Translation: DAA08956.1.

PIR

S38051.

RefSeq

NP_012709.1. NM_001179778.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3GAE	X-ray	1.60	A/B	464-715	[»]
3L3F	X-ray	1.90	X	354-715	[»]
3ODT	X-ray	1.35	A/B	2-300	[»]
3PSP	X-ray	2.42	A	325-715	[»]
3PST	X-ray	2.00	A	325-715	[»]

ProteinModelPortal

P36037.

SMR

P36037. Positions 2-295, 376-715.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6274N.

IntAct

P36037. 8 interactions.

MINT

MINT-606421.

STRING

4932.YKL213C.

Proteomic databases

PaxDb

P36037.

PeptideAtlas

P36037.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKL213C; YKL213C; YKL213C.

GeneID

853667.

KEGG

sce:YKL213C.

Organism-specific databases

CYGD

YKL213c.

SGD

S000001696. DOA1.

Phylogenomic databases

eggNOG

COG2319.

GeneTree

ENSGT00550000074944.

HOGENOM

HOG000174247.

KO

K14018.

OMA

HESFVYC.

OrthoDB

EOG4MGWGM.

Gene expression databases

Genevestigator

P36037.

GermOnline

YKL213C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

2.130.10.10. 2 hits.

InterPro

IPR020472. G-protein_beta_WD-40_rep.
IPR015155. PLAA_fam_Ub-bd_PFU.
IPR013535. PUL.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]

Pfam

PF09070. PFU. 1 hit.
PF08324. PUL. 1 hit.
PF00400. WD40. 5 hits.
[Graphical view]

PRINTS

PR00320. GPROTEINBRPT.

SMART

SM00320. WD40. 6 hits.
[Graphical view]

SUPFAM

SSF50978. WD40_like. 1 hit.

PROSITE

PS50176. ARM_REPEAT. False negative.
PS51394. PFU. 1 hit.
PS51396. PUL. 1 hit.
PS00678. WD_REPEATS_1. False negative.
PS50082. WD_REPEATS_2. 4 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P36037.

NextBio

974605.

Entry information

Entry name

DOA1_YEAST

Accession

Primary (citable) accession number: P36037
Secondary accession number(s): D6VWZ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	June 1, 1994
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