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Protein

ATP-dependent RNA helicase DOB1

Gene

MTR4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

ATP-dependent RNA helicase required for the 3'-end formation of 5.8S RNA. Cofactor for the exosome complex that unwinds secondary structure in pre-rRNA. Required for nucleocytoplasmic transport of mRNA. May serve as a chaperone which translocates or normalizes the structure of mRNAs in preparation for export. Component of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates.1 Publication

Miscellaneous

Present with 12500 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi171 – 178ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHelicase, Hydrolase
Biological processrRNA processing
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31514-MONOMER
BRENDAi3.6.4.13 984
ReactomeiR-SCE-429958 mRNA decay by 3' to 5' exoribonuclease
R-SCE-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DOB1 (EC:3.6.4.13)
Alternative name(s):
mRNA transport regulator MTR4
Gene namesi
Name:MTR4
Synonyms:DOB1
Ordered Locus Names:YJL050W
ORF Names:J1158
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJL050W
SGDiS000003586 MTR4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001020921 – 1073ATP-dependent RNA helicase DOB1Add BLAST1073

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei34PhosphothreonineCombined sources1
Modified residuei84PhosphoserineCombined sources1
Modified residuei843PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP47047
PaxDbiP47047
PRIDEiP47047

PTM databases

iPTMnetiP47047

Interactioni

Subunit structurei

Component of the TRAMP complex (also called TRF4 complex) composed of at least HUL4, MTR4, PAP2/TRF4 and either AIR1 or AIR2.1 Publication

Binary interactionsi

Protein-protein interaction databases

BioGridi33705, 262 interactors
ComplexPortaliCPX-1678 TRAMP complex variant 1
CPX-1679 TRAMP complex variant 2
CPX-1680 TRAMP5 complex
DIPiDIP-6394N
ELMiP47047
IntActiP47047, 19 interactors
MINTiP47047
STRINGi4932.YJL050W

Structurei

Secondary structure

11073
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP47047
SMRiP47047
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP47047

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini158 – 314Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST157
Domaini393 – 597Helicase C-terminalPROSITE-ProRule annotationAdd BLAST205

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi262 – 265DEVH box4

Sequence similaritiesi

Belongs to the helicase family. SKI2 subfamily.Curated

Phylogenomic databases

GeneTreeiENSGT00820000127042
HOGENOMiHOG000163047
InParanoidiP47047
KOiK12598
OMAiNMLYRGS
OrthoDBiEOG092C0MRM

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR011254 Prismane-like_sf
IPR025696 rRNA_proc-arch_dom
IPR016438 Ski2-like
IPR012961 Ski2_C
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF08148 DSHCT, 1 hit
PF00271 Helicase_C, 1 hit
PF13234 rRNA_proc-arch, 1 hit
PIRSFiPIRSF005198 Antiviral_helicase_SKI2, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM01142 DSHCT, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 3 hits
SSF56821 SSF56821, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit

Sequencei

Sequence statusi: Complete.

P47047-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDSTDLFDVF EETPVELPTD SNGEKNADTN VGDTPDHTQD KKHGLEEEKE
60 70 80 90 100
EHEENNSENK KIKSNKSKTE DKNKKVVVPV LADSFEQEAS REVDASKGLT
110 120 130 140 150
NSETLQVEQD GKVRLSHQVR HQVALPPNYD YTPIAEHKRV NEARTYPFTL
160 170 180 190 200
DPFQDTAISC IDRGESVLVS AHTSAGKTVV AEYAIAQSLK NKQRVIYTSP
210 220 230 240 250
IKALSNQKYR ELLAEFGDVG LMTGDITINP DAGCLVMTTE ILRSMLYRGS
260 270 280 290 300
EVMREVAWVI FDEVHYMRDK ERGVVWEETI ILLPDKVRYV FLSATIPNAM
310 320 330 340 350
EFAEWICKIH SQPCHIVYTN FRPTPLQHYL FPAHGDGIYL VVDEKSTFRE
360 370 380 390 400
ENFQKAMASI SNQIGDDPNS TDSRGKKGQT YKGGSAKGDA KGDIYKIVKM
410 420 430 440 450
IWKKKYNPVI VFSFSKRDCE ELALKMSKLD FNSDDEKEAL TKIFNNAIAL
460 470 480 490 500
LPETDRELPQ IKHILPLLRR GIGIHHSGLL PILKEVIEIL FQEGFLKVLF
510 520 530 540 550
ATETFSIGLN MPAKTVVFTS VRKWDGQQFR WVSGGEYIQM SGRAGRRGLD
560 570 580 590 600
DRGIVIMMID EKMEPQVAKG MVKGQADRLD SAFHLGYNMI LNLMRVEGIS
610 620 630 640 650
PEFMLEHSFF QFQNVISVPV MEKKLAELKK DFDGIEVEDE ENVKEYHEIE
660 670 680 690 700
QAIKGYREDV RQVVTHPANA LSFLQPGRLV EISVNGKDNY GWGAVVDFAK
710 720 730 740 750
RINKRNPSAV YTDHESYIVN VVVNTMYIDS PVNLLKPFNP TLPEGIRPAE
760 770 780 790 800
EGEKSICAVI PITLDSIKSI GNLRLYMPKD IRASGQKETV GKSLREVNRR
810 820 830 840 850
FPDGIPVLDP VKNMKIEDED FLKLMKKIDV LNTKLSSNPL TNSMRLEELY
860 870 880 890 900
GKYSRKHDLH EDMKQLKRKI SESQAVIQLD DLRRRKRVLR RLGFCTPNDI
910 920 930 940 950
IELKGRVACE ISSGDELLLT ELIFNGNFNE LKPEQAAALL SCFAFQERCK
960 970 980 990 1000
EAPRLKPELA EPLKAMREIA AKIAKIMKDS KIEVVEKDYV ESFRHELMEV
1010 1020 1030 1040 1050
VYEWCRGATF TQICKMTDVY EGSLIRMFKR LEELVKELVD VANTIGNSSL
1060 1070
KEKMEAVLKL IHRDIVSAGS LYL
Length:1,073
Mass (Da):122,055
Last modified:February 1, 1996 - v1
Checksum:i1FA9EAADC546F669
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49325 Genomic DNA Translation: CAA89341.1
BK006943 Genomic DNA Translation: DAA08749.1
PIRiS56822
RefSeqiNP_012485.1, NM_001181483.1

Genome annotation databases

EnsemblFungiiYJL050W; YJL050W; YJL050W
GeneIDi853397
KEGGisce:YJL050W

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49325 Genomic DNA Translation: CAA89341.1
BK006943 Genomic DNA Translation: DAA08749.1
PIRiS56822
RefSeqiNP_012485.1, NM_001181483.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XGJX-ray2.90A/B81-1073[»]
4QU4X-ray3.39A1-1073[»]
4U4CX-ray2.40A81-1073[»]
4WFDX-ray2.40C/F/I1-19[»]
5OOQX-ray3.20A/B81-1073[»]
6FSZelectron microscopy4.60MM1-1073[»]
6FT6electron microscopy3.90MM80-1073[»]
ProteinModelPortaliP47047
SMRiP47047
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33705, 262 interactors
ComplexPortaliCPX-1678 TRAMP complex variant 1
CPX-1679 TRAMP complex variant 2
CPX-1680 TRAMP5 complex
DIPiDIP-6394N
ELMiP47047
IntActiP47047, 19 interactors
MINTiP47047
STRINGi4932.YJL050W

PTM databases

iPTMnetiP47047

Proteomic databases

MaxQBiP47047
PaxDbiP47047
PRIDEiP47047

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJL050W; YJL050W; YJL050W
GeneIDi853397
KEGGisce:YJL050W

Organism-specific databases

EuPathDBiFungiDB:YJL050W
SGDiS000003586 MTR4

Phylogenomic databases

GeneTreeiENSGT00820000127042
HOGENOMiHOG000163047
InParanoidiP47047
KOiK12598
OMAiNMLYRGS
OrthoDBiEOG092C0MRM

Enzyme and pathway databases

BioCyciYEAST:G3O-31514-MONOMER
BRENDAi3.6.4.13 984
ReactomeiR-SCE-429958 mRNA decay by 3' to 5' exoribonuclease
R-SCE-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Miscellaneous databases

EvolutionaryTraceiP47047
PROiPR:P47047

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR011254 Prismane-like_sf
IPR025696 rRNA_proc-arch_dom
IPR016438 Ski2-like
IPR012961 Ski2_C
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF08148 DSHCT, 1 hit
PF00271 Helicase_C, 1 hit
PF13234 rRNA_proc-arch, 1 hit
PIRSFiPIRSF005198 Antiviral_helicase_SKI2, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM01142 DSHCT, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 3 hits
SSF56821 SSF56821, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiMTR4_YEAST
AccessioniPrimary (citable) accession number: P47047
Secondary accession number(s): D6VWD3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: September 12, 2018
This is version 171 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names
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