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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)DescriptionActionsGraphical viewLength
Nucleotide bindingi171 – 178ATPPROSITE-ProRule annotation8

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.

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)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.
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

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 interactors.
DIPiDIP-6394N.
IntActiP47047. 20 interactors.
MINTiMINT-620894.

Structurei

Secondary structure

11073
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 11Combined sources4
Beta strandi81 – 94Combined sources14
Beta strandi100 – 102Combined sources3
Beta strandi119 – 124Combined sources6
Helixi134 – 136Combined sources3
Helixi152 – 162Combined sources11
Beta strandi166 – 170Combined sources5
Helixi173 – 175Combined sources3
Helixi177 – 190Combined sources14
Beta strandi194 – 201Combined sources8
Helixi202 – 216Combined sources15
Beta strandi219 – 222Combined sources4
Beta strandi233 – 238Combined sources6
Helixi239 – 247Combined sources9
Helixi252 – 255Combined sources4
Beta strandi256 – 261Combined sources6
Helixi264 – 268Combined sources5
Turni270 – 272Combined sources3
Helixi273 – 282Combined sources10
Beta strandi288 – 293Combined sources6
Helixi299 – 310Combined sources12
Beta strandi314 – 319Combined sources6
Beta strandi326 – 332Combined sources7
Beta strandi336 – 342Combined sources7
Helixi350 – 361Combined sources12
Helixi393 – 403Combined sources11
Beta strandi408 – 412Combined sources5
Beta strandi413 – 415Combined sources3
Helixi416 – 426Combined sources11
Beta strandi427 – 429Combined sources3
Helixi434 – 448Combined sources15
Helixi453 – 456Combined sources4
Helixi459 – 462Combined sources4
Helixi465 – 469Combined sources5
Beta strandi472 – 475Combined sources4
Beta strandi477 – 479Combined sources3
Helixi481 – 492Combined sources12
Beta strandi497 – 501Combined sources5
Helixi503 – 507Combined sources5
Beta strandi513 – 519Combined sources7
Beta strandi521 – 524Combined sources4
Beta strandi526 – 531Combined sources6
Helixi534 – 541Combined sources8
Turni547 – 549Combined sources3
Beta strandi553 – 559Combined sources7
Helixi565 – 572Combined sources8
Helixi587 – 595Combined sources9
Beta strandi596 – 598Combined sources3
Helixi601 – 607Combined sources7
Helixi609 – 635Combined sources27
Helixi642 – 664Combined sources23
Helixi667 – 670Combined sources4
Helixi671 – 673Combined sources3
Beta strandi678 – 684Combined sources7
Turni685 – 687Combined sources3
Beta strandi688 – 700Combined sources13
Helixi713 – 715Combined sources3
Beta strandi716 – 727Combined sources12
Helixi732 – 734Combined sources3
Beta strandi755 – 763Combined sources9
Helixi764 – 766Combined sources3
Beta strandi767 – 774Combined sources8
Helixi786 – 800Combined sources15
Beta strandi801 – 803Combined sources3
Turni810 – 814Combined sources5
Helixi819 – 837Combined sources19
Helixi839 – 841Combined sources3
Beta strandi843 – 845Combined sources3
Helixi847 – 871Combined sources25
Helixi876 – 891Combined sources16
Helixi903 – 909Combined sources7
Helixi916 – 925Combined sources10
Turni926 – 930Combined sources5
Helixi933 – 944Combined sources12
Beta strandi950 – 952Combined sources3
Helixi957 – 979Combined sources23
Helixi986 – 992Combined sources7
Helixi998 – 1006Combined sources9
Helixi1010 – 1015Combined sources6
Helixi1021 – 1043Combined sources23
Turni1044 – 1046Combined sources3
Helixi1048 – 1061Combined sources14
Helixi1064 – 1067Combined sources4

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

Protein-protein interaction databases

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

PTM databases

iPTMnetiP47047.

Proteomic databases

MaxQBiP47047.
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.
OMAiDMKVQSS.
OrthoDBiEOG092C0MRM.

Enzyme and pathway databases

BioCyciYEAST:G3O-31514-MONOMER.
BRENDAi3.6.4.13. 984.

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: November 30, 2016
This is version 152 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.