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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: Annotation score: 5 out of 5-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

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi171 – 1788ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent 3'-5' RNA helicase activity Source: SGD
  • oxidoreductase activity Source: InterPro
  • poly(A) binding Source: SGD

GO - Biological processi

  • exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • ncRNA polyadenylation Source: SGD
  • nuclear mRNA surveillance of mRNA 3'-end processing Source: SGD
  • nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  • nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription Source: SGD
  • polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  • rRNA catabolic process Source: SGD
  • U4 snRNA 3'-end processing Source: SGD
  • U5 snRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31514-MONOMER.
BRENDAi3.6.4.13. 984.
ReactomeiR-SCE-6791226. Major pathway of rRNA processing in the nucleolus.

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

GO - Cellular componenti

  • nucleolus Source: SGD
  • nucleus Source: SGD
  • TRAMP complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10731073ATP-dependent RNA helicase DOB1PRO_0000102092Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei34 – 341PhosphothreonineCombined sources
Modified residuei84 – 841PhosphoserineCombined sources
Modified residuei843 – 8431PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP47047.

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

WithEntry#Exp.IntActNotes
AIR2Q124766EBI-11592,EBI-31475
HMT1P380742EBI-11592,EBI-8394
PAP2P5363210EBI-11592,EBI-19517
TRF5P485616EBI-11592,EBI-19525

Protein-protein interaction databases

BioGridi33705. 110 interactions.
DIPiDIP-6394N.
IntActiP47047. 20 interactions.
MINTiMINT-620894.

Structurei

Secondary structure

1
1073
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi8 – 114Combined sources
Beta strandi81 – 9414Combined sources
Beta strandi100 – 1023Combined sources
Beta strandi119 – 1246Combined sources
Helixi134 – 1363Combined sources
Helixi152 – 16211Combined sources
Beta strandi166 – 1705Combined sources
Helixi173 – 1753Combined sources
Helixi177 – 19014Combined sources
Beta strandi194 – 2018Combined sources
Helixi202 – 21615Combined sources
Beta strandi219 – 2224Combined sources
Beta strandi233 – 2386Combined sources
Helixi239 – 2479Combined sources
Helixi252 – 2554Combined sources
Beta strandi256 – 2616Combined sources
Helixi264 – 2685Combined sources
Turni270 – 2723Combined sources
Helixi273 – 28210Combined sources
Beta strandi288 – 2936Combined sources
Helixi299 – 31012Combined sources
Beta strandi314 – 3196Combined sources
Beta strandi326 – 3327Combined sources
Beta strandi336 – 3427Combined sources
Helixi350 – 36112Combined sources
Helixi393 – 40311Combined sources
Beta strandi408 – 4125Combined sources
Beta strandi413 – 4153Combined sources
Helixi416 – 42611Combined sources
Beta strandi427 – 4293Combined sources
Helixi434 – 44815Combined sources
Helixi453 – 4564Combined sources
Helixi459 – 4624Combined sources
Helixi465 – 4695Combined sources
Beta strandi472 – 4754Combined sources
Beta strandi477 – 4793Combined sources
Helixi481 – 49212Combined sources
Beta strandi497 – 5015Combined sources
Helixi503 – 5075Combined sources
Beta strandi513 – 5197Combined sources
Beta strandi521 – 5244Combined sources
Beta strandi526 – 5316Combined sources
Helixi534 – 5418Combined sources
Turni547 – 5493Combined sources
Beta strandi553 – 5597Combined sources
Helixi565 – 5728Combined sources
Helixi587 – 5959Combined sources
Beta strandi596 – 5983Combined sources
Helixi601 – 6077Combined sources
Helixi609 – 63527Combined sources
Helixi642 – 66423Combined sources
Helixi667 – 6704Combined sources
Helixi671 – 6733Combined sources
Beta strandi678 – 6847Combined sources
Turni685 – 6873Combined sources
Beta strandi688 – 70013Combined sources
Helixi713 – 7153Combined sources
Beta strandi716 – 72712Combined sources
Helixi732 – 7343Combined sources
Beta strandi755 – 7639Combined sources
Helixi764 – 7663Combined sources
Beta strandi767 – 7748Combined sources
Helixi786 – 80015Combined sources
Beta strandi801 – 8033Combined sources
Turni810 – 8145Combined sources
Helixi819 – 83719Combined sources
Helixi839 – 8413Combined sources
Beta strandi843 – 8453Combined sources
Helixi847 – 87125Combined sources
Helixi876 – 89116Combined sources
Helixi903 – 9097Combined sources
Helixi916 – 92510Combined sources
Turni926 – 9305Combined sources
Helixi933 – 94412Combined sources
Beta strandi950 – 9523Combined sources
Helixi957 – 97923Combined sources
Helixi986 – 9927Combined sources
Helixi998 – 10069Combined sources
Helixi1010 – 10156Combined sources
Helixi1021 – 104323Combined sources
Turni1044 – 10463Combined sources
Helixi1048 – 106114Combined sources
Helixi1064 – 10674Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2XGJX-ray2.90A/B81-1073[»]
4QU4X-ray3.39A1-1073[»]
4U4CX-ray2.40A81-1073[»]
4WFDX-ray2.40C/F/I1-19[»]
ProteinModelPortaliP47047.
SMRiP47047. Positions 80-1071.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP47047.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini158 – 314157Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini393 – 597205Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi262 – 2654DEVH box

Sequence similaritiesi

Belongs to the helicase family. SKI2 subfamily.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00820000127042.
HOGENOMiHOG000163047.
InParanoidiP47047.
KOiK12598.
OMAiDMKVQSS.
OrthoDBiEOG092C0MRM.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR011254. Prismane-like.
IPR025696. rRNA_proc-arch_dom.
IPR016438. Ski2.
IPR012961. Ski2_C.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF08148. DSHCT. 1 hit.
PF00271. Helicase_C. 1 hit.
PF13234. rRNA_proc-arch. 1 hit.
[Graphical view]
PIRSFiPIRSF005198. Antiviral_helicase_SKI2. 1 hit.
SMARTiSM00487. DEXDc. 1 hit.
SM01142. DSHCT. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
SSF56821. SSF56821. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

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.

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2XGJX-ray2.90A/B81-1073[»]
4QU4X-ray3.39A1-1073[»]
4U4CX-ray2.40A81-1073[»]
4WFDX-ray2.40C/F/I1-19[»]
ProteinModelPortaliP47047.
SMRiP47047. Positions 80-1071.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33705. 110 interactions.
DIPiDIP-6394N.
IntActiP47047. 20 interactions.
MINTiMINT-620894.

PTM databases

iPTMnetiP47047.

Proteomic databases

MaxQBiP47047.

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.
OMAiDMKVQSS.
OrthoDBiEOG092C0MRM.

Enzyme and pathway databases

BioCyciYEAST:G3O-31514-MONOMER.
BRENDAi3.6.4.13. 984.
ReactomeiR-SCE-6791226. Major pathway of rRNA processing in the nucleolus.

Miscellaneous databases

EvolutionaryTraceiP47047.
PROiP47047.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR011254. Prismane-like.
IPR025696. rRNA_proc-arch_dom.
IPR016438. Ski2.
IPR012961. Ski2_C.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF08148. DSHCT. 1 hit.
PF00271. Helicase_C. 1 hit.
PF13234. rRNA_proc-arch. 1 hit.
[Graphical view]
PIRSFiPIRSF005198. Antiviral_helicase_SKI2. 1 hit.
SMARTiSM00487. DEXDc. 1 hit.
SM01142. DSHCT. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
SSF56821. SSF56821. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMTR4_YEAST
AccessioniPrimary (citable) accession number: P47047
Secondary accession number(s): D6VWD3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: September 7, 2016
This is version 149 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.