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Protein

ATP-dependent RNA helicase SUB2

Gene

SUB2

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-binding RNA helicase component of the TREX complex involved in transcription elongation and required for the export of mRNA out of the nucleus. SUB2 plays also a role in pre-mRNA splicing and spliceosome assembly. May be involved in rDNA and telomeric silencing, and maintenance of genome integrity.13 Publications

Miscellaneous

Present with 51700 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi106 – 113ATP8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: SGD
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • chromatin silencing at telomere Source: SGD
  • mRNA 3'-end processing Source: SGD
  • mRNA export from nucleus Source: SGD
  • mRNA splicing, via spliceosome Source: SGD
  • RNA secondary structure unwinding Source: GO_Central
  • transcription-coupled nucleotide-excision repair Source: SGD
  • transcription elongation from RNA polymerase II promoter Source: SGD

Keywordsi

Molecular functionHelicase, Hydrolase, RNA-binding
Biological processmRNA processing, mRNA splicing, mRNA transport, Transport
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29493-MONOMER.

Protein family/group databases

TCDBi3.A.22.1.1. the transcription-coupled trex/tap nuclear mrna export complex (trex) family.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase SUB2 (EC:3.6.4.13)
Alternative name(s):
Suppressor of BRR1 protein 2
Gene namesi
Name:SUB2
Ordered Locus Names:YDL084W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL084W.
SGDiS000002242. SUB2.

Subcellular locationi

GO - Cellular componenti

  • chromosome, telomeric region Source: SGD
  • nucleolus Source: GO_Central
  • spliceosomal complex Source: SGD
  • transcription export complex Source: SGD

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi8D → G: No growth at 37 degrees Celsius; when associated with DEL-135. 1 Publication1
Mutagenesisi22D → G in SUB2-1; no growth at 16 and 37 degrees Celsius; when associated with G-83; M-142 and T-146. 1 Publication1
Mutagenesisi83E → G in SUB2-1; no growth at 16 and 37 degrees Celsius; when associated with G-22; M-142 and T-146. 1 Publication1
Mutagenesisi112K → N: Lethal. 1 Publication1
Mutagenesisi122Q → R in SUB2-201; no growth at 37 degrees Celsius; when associated with G-173 and F-403. 1 Publication1
Mutagenesisi135Missing : No growth at 37 degrees Celsius; when associated with G-8. 1 Publication1
Mutagenesisi142L → M in SUB2-1; no growth at 16 and 37 degrees Celsius; when associated with G-22; G-83 and T-146. 1 Publication1
Mutagenesisi146I → T in SUB2-1; no growth at 16 and 37 degrees Celsius; when associated with G-22; G-83 and M-142. 1 Publication1
Mutagenesisi173K → G in SUB2-201; no growth at 37 degrees Celsius; when associated with R-122 and F-403. 1 Publication1
Mutagenesisi174D → G in SUB2-100; no growth at 37 degrees Celsius. 1 Publication1
Mutagenesisi215D → E: Lethal. 1 Publication1
Mutagenesisi217C → A: Lethal. 1 Publication1
Mutagenesisi247S → L: Lethal. 1 Publication1
Mutagenesisi308Q → R in SUB2-5; no growth at 16 degrees Celsius. 1 Publication1
Mutagenesisi403K → F in SUB2-201; no growth at 37 degrees Celsius; when associated with R-122 and G-173. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000550822 – 446ATP-dependent RNA helicase SUB2Add BLAST445

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei13PhosphoserineCombined sources1
Modified residuei37PhosphoserineCombined sources1
Modified residuei169PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ07478.
PRIDEiQ07478.

PTM databases

iPTMnetiQ07478.

Interactioni

Subunit structurei

Component of the TREX complex composed of at least SUB2, TEX1, YRA1 and the four THO complex components: HPR1, MFT1, THO2 and THP1. Interacts with HPR1, YRA1, and YRA2. SUB2 may mediate the interaction between the THO complex and YRA1. Associates with growing mRNP complexes during transcription. This association requires the presence of HPR1. Interacts also with SAC3.4 Publications

Protein-protein interaction databases

BioGridi31977. 225 interactors.
DIPiDIP-5343N.
IntActiQ07478. 26 interactors.
MINTiMINT-526164.
STRINGi4932.YDL084W.

Structurei

Secondary structure

1446
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi63 – 67Combined sources5
Helixi71 – 79Combined sources9
Helixi87 – 96Combined sources10
Turni97 – 99Combined sources3
Beta strandi102 – 105Combined sources4
Beta strandi110 – 112Combined sources3
Helixi113 – 123Combined sources11
Beta strandi133 – 136Combined sources4
Helixi140 – 153Combined sources14
Turni154 – 156Combined sources3
Beta strandi162 – 165Combined sources4
Helixi171 – 179Combined sources9
Turni181 – 183Combined sources3
Beta strandi186 – 190Combined sources5
Helixi192 – 199Combined sources8
Turni200 – 202Combined sources3
Beta strandi211 – 215Combined sources5
Helixi217 – 222Combined sources6
Helixi224 – 234Combined sources11
Beta strandi239 – 248Combined sources10
Turni252 – 254Combined sources3
Helixi255 – 259Combined sources5
Beta strandi266 – 268Combined sources3
Helixi273 – 276Combined sources4
Beta strandi281 – 287Combined sources7
Helixi290 – 292Combined sources3
Helixi293 – 303Combined sources11
Beta strandi307 – 312Combined sources6
Helixi316 – 328Combined sources13
Beta strandi333 – 336Combined sources4
Beta strandi338 – 340Combined sources3
Helixi342 – 353Combined sources12
Beta strandi358 – 362Combined sources5
Helixi364 – 366Combined sources3
Beta strandi367 – 369Combined sources3
Beta strandi375 – 382Combined sources8
Helixi387 – 394Combined sources8
Helixi399 – 401Combined sources3
Beta strandi404 – 410Combined sources7
Helixi413 – 426Combined sources14
Helixi441 – 443Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5SUPX-ray2.60A/B/C61-446[»]
5SUQX-ray6.00A/C1-446[»]
ProteinModelPortaliQ07478.
SMRiQ07478.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 268Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST176
Domaini280 – 441Helicase C-terminalPROSITE-ProRule annotationAdd BLAST162

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi62 – 90Q motifAdd BLAST29
Motifi215 – 218DECD box4

Domaini

The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00830000128348.
HOGENOMiHOG000268797.
InParanoidiQ07478.
KOiK12812.
OMAiIICQAKS.
OrthoDBiEOG092C2V3O.

Family and domain databases

InterProiView protein in InterPro
IPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR014014. RNA_helicase_DEAD_Q_motif.
PfamiView protein in Pfam
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
SMARTiView protein in SMART
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiView protein in PROSITE
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q07478-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSHEGEEDLL EYSDNEQEIQ IDASKAAEAG ETGAATSATE GDNNNNTAAG
60 70 80 90 100
DKKGSYVGIH STGFKDFLLK PELSRAIIDC GFEHPSEVQQ HTIPQSIHGT
110 120 130 140 150
DVLCQAKSGL GKTAVFVLST LQQLDPVPGE VAVVVICNAR ELAYQIRNEY
160 170 180 190 200
LRFSKYMPDV KTAVFYGGTP ISKDAELLKN KDTAPHIVVA TPGRLKALVR
210 220 230 240 250
EKYIDLSHVK NFVIDECDKV LEELDMRRDV QEIFRATPRD KQVMMFSATL
260 270 280 290 300
SQEIRPICRR FLQNPLEIFV DDEAKLTLHG LQQYYIKLEE REKNRKLAQL
310 320 330 340 350
LDDLEFNQVI IFVKSTTRAN ELTKLLNASN FPAITVHGHM KQEERIARYK
360 370 380 390 400
AFKDFEKRIC VSTDVFGRGI DIERINLAIN YDLTNEADQY LHRVGRAGRF
410 420 430 440
GTKGLAISFV SSKEDEEVLA KIQERFDVKI AEFPEEGIDP STYLNN
Length:446
Mass (Da):50,309
Last modified:November 1, 1996 - v1
Checksum:iAB3605A8C38A560C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74132 Genomic DNA. Translation: CAA98650.1.
AY692907 Genomic DNA. Translation: AAT92926.1.
BK006938 Genomic DNA. Translation: DAA11775.1.
PIRiS67620.
RefSeqiNP_010199.1. NM_001180143.1.

Genome annotation databases

EnsemblFungiiYDL084W; YDL084W; YDL084W.
GeneIDi851475.
KEGGisce:YDL084W.

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.

Entry informationi

Entry nameiSUB2_YEAST
AccessioniPrimary (citable) accession number: Q07478
Secondary accession number(s): D6VRR5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: July 5, 2017
This is version 172 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. 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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names