P39517 (DHH1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent RNA helicase DHH1
EC=3.6.4.13

Alternative name(s):
DExD/H-box helicase 1

Gene names

Name:	DHH1
Ordered Locus Names:	YDL160C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	506 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	ATP-dependent RNA helicase involved in mRNA turnover, and more specifically in mRNA decapping by activating the decapping enzyme DCP1. Is involved in G1/S DNA-damage checkpoint recovery, probably through the regulation of the translational status of a subset of mRNAs. May also have a role in translation and mRNA nuclear export. Required for sporulation. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.11 Ref.12 Ref.13 Ref.14
Catalytic activity	ATP + H2O = ADP + phosphate.
Subunit structure	Associated with the CCR4-NOT complex and possibly other big complexes. Interacts with CDC39/NOT1 and POP2, components of the CCR4-NOT complex, with the mRNA decapping proteins DCP1, LSM1, PAT1, and with KEM1, the major 5'-3' exonuclease. Ref.4 Ref.5 Ref.6 Ref.7
Subcellular location	Cytoplasm › P-body. Note: Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bodies) which represent sites of mRNA decapping and 5' to 3' exonucleotidic decay. Ref.6 Ref.8 Ref.9 Ref.11 Ref.14
Domain	The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.
Miscellaneous	Present with 42900 molecules/cell in log phase SD medium. Ref.10
Sequence similarities	Belongs to the DEAD box helicase family. DDX6/DHH1 subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Biological process	Translation regulation Transport mRNA processing mRNA transport
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cell morphogenesis involved in conjugation with cellular fusion Inferred from mutant phenotype. Source: SGD cytoplasmic mRNA processing body assembly Inferred from mutant phenotype. Source: SGD deadenylation-dependent decapping of nuclear-transcribed mRNA Inferred from mutant phenotype Ref.5. Source: SGD mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW mRNA transport Inferred from electronic annotation. Source: UniProtKB-KW regulation of translation Inferred from electronic annotation. Source: UniProtKB-KW stress granule assembly Inferred from mutant phenotype. Source: SGD
Cellular component	cytoplasmic mRNA processing body Inferred from direct assay Ref.11. Source: SGD cytoplasmic stress granule Inferred from direct assay. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction Ref.5. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
EDC3	P39998	3	EBI-158,EBI-22300
LSM1	P47017	3	EBI-158,EBI-174
LSM2	P38203	3	EBI-158,EBI-180
LSM4	P40070	3	EBI-158,EBI-188
LSM7	P53905	3	EBI-158,EBI-141
PAT1	P25644	5	EBI-158,EBI-204
POP2	P39008	3	EBI-158,EBI-13629

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 506

506

ATP-dependent RNA helicase DHH1

PRO_0000055044

Regions

Domain

77 – 247

171

Helicase ATP-binding

Domain

257 – 417

161

Helicase C-terminal

Nucleotide binding

90 – 97

8

ATP By similarity

Motif

46 – 74

29

Q motif

Motif

195 – 198

4

DEAD box

Compositional bias

434 – 505

72

Gln-rich

Amino acid modifications

Modified residue

16

1

Phosphothreonine Ref.15

Experimental info

Mutagenesis

89

1

R → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius; when associated with A-91. Impairs RNA binding in vitro. Ref.16

Mutagenesis

91

1

K → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius; when associated with A-89. Impairs RNA binding in vitro. Ref.16

Mutagenesis

195

1

D → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius. Ref.16

Mutagenesis

196

1

E → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius. Ref.16

Mutagenesis

345

1

R → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius. Impairs RNA binding in vitro. Ref.16

Mutagenesis

346

1

G → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius. Impairs RNA binding in vitro. Ref.16

Mutagenesis

369

1

H → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius. Ref.16

Mutagenesis

370

1

R → A: Leads to mRNA turnover defect and no growth at 37 degrees Celsius. Impairs RNA binding in vitro. Ref.16

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

506

Helix Strand Turn

Details...

Helix

48 – 51

4

Helix

55 – 63

9

Helix

71 – 82

12

Beta strand

86 – 89

4

Helix

96 – 107

12

Beta strand

117 – 120

4

Helix

124 – 137

14

Turn

138 – 142

5

Beta strand

145 – 148

4

Beta strand

150 – 152

3

Helix

154 – 160

7

Beta strand

166 – 170

5

Helix

172 – 180

9

Beta strand

191 – 196

6

Helix

197 – 200

4

Helix

203 – 213

11

Beta strand

221 – 227

7

Helix

231 – 240

10

Beta strand

245 – 248

4

Beta strand

258 – 264

7

Helix

267 – 269

3

Helix

270 – 280

11

Beta strand

284 – 289

6

Helix

293 – 306

14

Beta strand

310 – 313

4

Helix

319 – 330

12

Beta strand

333 – 341

9

Beta strand

343 – 346

4

Beta strand

352 – 359

8

Helix

364 – 371

8

Beta strand

373 – 375

3

Beta strand

381 – 387

7

Helix

389 – 391

3

Helix

392 – 402

11

Helix

415 – 417

3

Sequences

	Sequence		Length	Mass (Da)
	P39517 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 062CFA56DF6F2CEE	FASTA	506	57,544
	10 20 30 40 50 60 MGSINNNFNT NNNSNTDLDR DWKTALNIPK KDTRPQTDDV LNTKGNTFED FYLKRELLMG 70 80 90 100 110 120 IFEAGFEKPS PIQEEAIPVA ITGRDILARA KNGTGKTAAF VIPTLEKVKP KLNKIQALIM 130 140 150 160 170 180 VPTRELALQT SQVVRTLGKH CGISCMVTTG GTNLRDDILR LNETVHILVG TPGRVLDLAS 190 200 210 220 230 240 RKVADLSDCS LFIMDEADKM LSRDFKTIIE QILSFLPPTH QSLLFSATFP LTVKEFMVKH 250 260 270 280 290 300 LHKPYEINLM EELTLKGITQ YYAFVEERQK LHCLNTLFSK LQINQAIIFC NSTNRVELLA 310 320 330 340 350 360 KKITDLGYSC YYSHARMKQQ ERNKVFHEFR QGKVRTLVCS DLLTRGIDIQ AVNVVINFDF 370 380 390 400 410 420 PKTAETYLHR IGRSGRFGHL GLAINLINWN DRFNLYKIEQ ELGTEIAAIP ATIDKSLYVA 430 440 450 460 470 480 ENDETVPVPF PIEQQSYHQQ AIPQQQLPSQ QQFAIPPQQH HPQFMVPPSH QQQQAYPPPQ 490 500 MPSQQGYPPQ QEHFMAMPPG QSQPQY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A yeast gene encoding a putative RNA helicase of the 'DEAD'-box family." Strahl-Bolsinger S., Tanner W. Yeast 9:429-432(1993) [PubMed: 8511971] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Dhh1p, a putative RNA helicase, associates with the general transcription factors Pop2p and Ccr4p from Saccharomyces cerevisiae." Hata H., Mitsui H., Liu H., Bai Y., Denis C.L., Shimizu Y., Sakai A. Genetics 148:571-579(1998) [PubMed: 9504907] [Abstract] Cited for: FUNCTION, INTERACTION WITH POP2, ASSOCIATION WITH THE CCR4-NOT COMPLEX.
[5]	"The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes." Coller J.M., Tucker M., Sheth U., Valencia-Sanchez M.A., Parker R. RNA 7:1717-1727(2001) [PubMed: 11780629] [Abstract] Cited for: FUNCTION, INTERACTION WITH DCP1; LSM1; PAT1 AND POP2.
[6]	"The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1." Fischer N., Weis K. EMBO J. 21:2788-2797(2002) [PubMed: 12032091] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH KEM1 AND PAT1.
[7]	"Interaction between Not1p, a component of the Ccr4-not complex, a global regulator of transcription, and Dhh1p, a putative RNA helicase." Maillet L., Collart M.A. J. Biol. Chem. 277:2835-2842(2002) [PubMed: 11696541] [Abstract] Cited for: FUNCTION, INTERACTION WITH CDC39.
[8]	"Functional conservation of Dhh1p, a cytoplasmic DExD/H-box protein present in large complexes." Tseng-Rogenski S.S.-I., Chong J.-L., Thomas C.B., Enomoto S., Berman J., Chang T.-H. Nucleic Acids Res. 31:4995-5002(2003) [PubMed: 12930949] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, ASSOCIATION WITH LARGE COMPLEXES.
[9]	"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: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[10]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]	"Decapping and decay of messenger RNA occur in cytoplasmic processing bodies." Sheth U., Parker R. Science 300:805-808(2003) [PubMed: 12730603] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[12]	"An essential role for the Saccharomyces cerevisiae DEAD-box helicase DHH1 in G1/S DNA-damage checkpoint recovery." Bergkessel M., Reese J.C. Genetics 167:21-33(2004) [PubMed: 15166134] [Abstract] Cited for: FUNCTION.
[13]	"Processing bodies require RNA for assembly and contain nontranslating mRNAs." Teixeira D., Sheth U., Valencia-Sanchez M.A., Brengues M., Parker R. RNA 11:371-382(2005) [PubMed: 15703442] [Abstract] Cited for: FUNCTION.
[14]	"The yeast EDC1 mRNA undergoes deadenylation-independent decapping stimulated by Not2p, Not4p, and Not5p." Muhlrad D., Parker R. EMBO J. 24:1033-1045(2005) [PubMed: 15706350] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[15]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16, MASS SPECTROMETRY.
[16]	"Crystal structure and functional analysis of DEAD-box protein Dhh1p." Cheng Z., Coller J.M., Parker R., Song H. RNA 11:1258-1270(2005) [PubMed: 15987810] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 31-425, MUTAGENESIS OF ARG-89; LYS-91; ASP-195; GLU-196; ARG-345; GLY-346; HIS-369 AND ARG-370.
+	Additional computationally mapped references.

Web resources

RNA helicases from the baker's yeast Saccharomyces cerevisiae

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X66057 Genomic DNA. Translation: CAA46853.1.
Z67750 Genomic DNA. Translation: CAA91586.1.
Z74208 Genomic DNA. Translation: CAA98734.1.
BK006938 Genomic DNA. Translation: DAA11700.1.

PIR

S31229.

RefSeq

NP_010121.1. NM_001180220.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1S2M	X-ray	2.10	A	31-425	[»]

ProteinModelPortal

P39517.

SMR

P39517. Positions 46-422.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1243N.

IntAct

P39517. 39 interactions.

MINT

MINT-385061.

STRING

P39517.

Proteomic databases

PeptideAtlas

P39517.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL160C; YDL160C; YDL160C.

GeneID

851394.

KEGG

sce:YDL160C.

NMPDR

fig|4932.3.peg.856.

Organism-specific databases

CYGD

YDL160c.

SGD

S000002319. DHH1.

Phylogenomic databases

eggNOG

fuNOG04494.

GeneTree

EFGT00050000000529.

HOGENOM

HBG737336.

OMA

FHDFRQG.

OrthoDB

EOG4QJVWF.

Gene expression databases

ArrayExpress

P39517.

Genevestigator

P39517.

GermOnline

YDL160C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR014001. DEAD-like_helicase.
IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR001650. Helicase_C.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]

KO

K12614.

Pfam

PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

PROSITE

PS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

968552.

Entry information

Entry name

DHH1_YEAST

Accession

Primary (citable) accession number: P39517
Secondary accession number(s): D6VRJ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	December 14, 2011
This is version 117 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program