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Protein

Transcription elongation factor SPT5

Gene

SPT5

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

The SPT4-SPT5 complex mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing. This complex seems to be important for the stability of the RNA polymerase II elongation machinery on the chromatin template but not for the inherent ability of this machinery to translocate down the gene.5 Publications

GO - Molecular functioni

  • RNA polymerase I core binding Source: SGD
  • RNA polymerase II core binding Source: SGD
  • RNA polymerase I transcription factor binding Source: SGD
  • rRNA binding Source: SGD
  • transcription factor activity, core RNA polymerase I binding Source: SGD
  • transcription factor activity, core RNA polymerase II binding Source: SGD

GO - Biological processi

  • 7-methylguanosine mRNA capping Source: SGD
  • intracellular mRNA localization Source: SGD
  • mRNA splicing, via spliceosome Source: SGD
  • negative regulation of transcription elongation from RNA polymerase I promoter Source: SGD
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  • positive regulation of transcription elongation from RNA polymerase I promoter Source: SGD
  • regulation of rRNA processing Source: SGD
  • regulation of transcription-coupled nucleotide-excision repair Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

mRNA processing, Transcription

Enzyme and pathway databases

BioCyciYEAST:G3O-32614-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-72086. mRNA Capping.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription elongation factor SPT5
Alternative name(s):
Chromatin elongation factor SPT5
Gene namesi
Name:SPT5
Ordered Locus Names:YML010W
ORF Names:YM9571.08
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YML010W.
SGDiS000004470. SPT5.

Subcellular locationi

GO - Cellular componenti

  • DSIF complex Source: SGD
  • mitochondrion Source: UniProtKB-SubCell
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10631063Transcription elongation factor SPT5PRO_0000208477Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei35 – 351PhosphothreonineCombined sources
Modified residuei133 – 1331PhosphothreonineCombined sources
Modified residuei136 – 1361PhosphoserineCombined sources
Modified residuei188 – 1881PhosphoserineCombined sources
Modified residuei219 – 2191PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP27692.
PeptideAtlasiP27692.
PRIDEiP27692.

PTM databases

iPTMnetiP27692.

Interactioni

Subunit structurei

Component of the SPT4-SPT5 complex. Interacts with RNA polymerase II. Interacts with SHE2.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CDC73Q066976EBI-17937,EBI-29913
CTR9P891052EBI-17937,EBI-5283
PSY2P401646EBI-17937,EBI-29107
RPO21P040503EBI-17937,EBI-15760
RTF1P530645EBI-17937,EBI-16303
SPT4P329148EBI-17937,EBI-17928
SPT6P236152EBI-17937,EBI-17947

GO - Molecular functioni

  • RNA polymerase I core binding Source: SGD
  • RNA polymerase II core binding Source: SGD
  • RNA polymerase I transcription factor binding Source: SGD

Protein-protein interaction databases

BioGridi35159. 170 interactions.
DIPiDIP-6621N.
IntActiP27692. 89 interactions.
MINTiMINT-631921.

Structurei

Secondary structure

1
1063
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi387 – 3904Combined sources
Turni394 – 3974Combined sources
Beta strandi399 – 4057Combined sources
Beta strandi409 – 4168Combined sources
Turni422 – 4254Combined sources
Helixi442 – 4443Combined sources
Helixi453 – 4608Combined sources
Helixi461 – 4633Combined sources
Beta strandi464 – 4685Combined sources
Beta strandi471 – 4744Combined sources
Beta strandi477 – 4804Combined sources
Beta strandi483 – 4897Combined sources
Helixi490 – 4923Combined sources
Helixi502 – 5076Combined sources
Beta strandi539 – 5424Combined sources
Turni546 – 5494Combined sources
Beta strandi551 – 56616Combined sources
Beta strandi573 – 5764Combined sources
Helixi577 – 5793Combined sources
Beta strandi580 – 5823Combined sources
Beta strandi589 – 5924Combined sources
Turni596 – 5994Combined sources
Beta strandi601 – 6088Combined sources
Beta strandi611 – 6166Combined sources
Turni617 – 6193Combined sources
Beta strandi620 – 6267Combined sources
Helixi627 – 6293Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EXUX-ray2.23A285-375[»]
4YTKX-ray1.09A382-511[»]
4YTLX-ray1.60A/B534-632[»]
ProteinModelPortaliP27692.
SMRiP27692. Positions 270-375, 382-508, 534-632, 800-847.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP27692.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini382 – 41534KOW 1Add
BLAST
Domaini533 – 56028KOW 2Add
BLAST
Domaini584 – 61532KOW 3Add
BLAST
Domaini799 – 83234KOW 4Add
BLAST
Repeati931 – 93661
Repeati937 – 94262
Repeati948 – 95363
Repeati958 – 96364
Repeati969 – 97465
Repeati975 – 98066
Repeati981 – 98667
Repeati987 – 99268
Repeati1000 – 100569
Repeati1009 – 1014610
Repeati1015 – 1020611
Repeati1032 – 1037612
Repeati1043 – 1048613
Repeati1052 – 1057614
Repeati1058 – 1063615

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni931 – 106313315 X 6 AA tandem repeats of S-[TA]-W-G-G-[AQ]Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi148 – 16720Asp/Glu-rich (acidic)Add
BLAST
Compositional biasi189 – 19911Asp/Glu-rich (acidic)Add
BLAST

Domaini

The carboxy-terminal repeats are critical for activity.

Sequence similaritiesi

Belongs to the SPT5 family.Curated
Contains 4 KOW domains.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00440000037640.
HOGENOMiHOG000189404.
InParanoidiP27692.
KOiK15172.
OMAiTQCRTIS.
OrthoDBiEOG77WWNF.

Family and domain databases

InterProiIPR005824. KOW.
IPR006645. NGN_dom.
IPR024945. Spt5_C_dom.
IPR022581. Spt5_N.
IPR017071. TF_Spt5.
IPR005100. TF_Spt5_NGN-domain.
IPR008991. Translation_prot_SH3-like.
[Graphical view]
PfamiPF03439. Spt5-NGN. 1 hit.
PF11942. Spt5_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036945. Spt5. 1 hit.
SMARTiSM01104. CTD. 1 hit.
SM00739. KOW. 4 hits.
SM00738. NGN. 1 hit.
[Graphical view]
SUPFAMiSSF50104. SSF50104. 2 hits.

Sequencei

Sequence statusi: Complete.

P27692-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDNSDTNVS MQDHDQQFAD PVVVPQSTDT KDENTSDKDT VDSGNVTTTE
60 70 80 90 100
STERAESTSN IPPLDGEEKE AKSEPQQPED NAETAATEQV SSSNGPATDD
110 120 130 140 150
AQATLNTDSS EANEIVKKEE GSDERKRPRE EDTKNSDGDT KDEGDNKDED
160 170 180 190 200
DDEDDDDDDD DEDDDDEAPT KRRRQERNRF LDIEAEVSDD EDEDEDEEDS
210 220 230 240 250
ELVREGFITH GDDEDDEASA PGARRDDRLH RQLDQDLNKT SEEDAQRLAK
260 270 280 290 300
ELRERYGRSS SKQYRAAAQD GYVPQRFLLP SVDTATIWGV RCRPGKEKEL
310 320 330 340 350
IRKLLKKKFN LDRAMGKKKL KILSIFQRDN YTGRIYIEAP KQSVIEKFCN
360 370 380 390 400
GVPDIYISQK LLIPVQELPL LLKPNKSDDV ALEEGSYVRI KRGIYKGDLA
410 420 430 440 450
MVDQISENNL EVMLKIVPRL DYGKFDEIDP TTQQRKSRRP TFAHRAPPQL
460 470 480 490 500
FNPTMALRLD QANLYKRDDR HFTYKNEDYI DGYLYKSFRI QHVETKNIQP
510 520 530 540 550
TVEELARFGS KEGAVDLTSV SQSIKKAQAA KVTFQPGDRI EVLNGEQRGS
560 570 580 590 600
KGIVTRTTKD IATIKLNGFT TPLEFPISTL RKIFEPGDHV TVINGEHQGD
610 620 630 640 650
AGLVLMVEQG QVTFMSTQTS REVTITANNL SKSIDTTATS SEYALHDIVE
660 670 680 690 700
LSAKNVACII QAGHDIFKVI DETGKVSTIT KGSILSKINT ARARVSSVDA
710 720 730 740 750
NGNEIKIGDT IVEKVGSRRE GQVLYIQTQQ IFVVSKKIVE NAGVFVVNPS
760 770 780 790 800
NVEAVASKDN MLSNKMDLSK MNPEIISKMG PPSSKTFQQP IQSRGGREVA
810 820 830 840 850
LGKTVRIRSA GYKGQLGIVK DVNGDKATVE LHSKNKHITI DKHKLTYYNR
860 870 880 890 900
EGGEGITYDE LVNRRGRVPQ ARMGPSYVSA PRNMATGGIA AGAAATSSGL
910 920 930 940 950
SGGMTPGWSS FDGGKTPAVN AHGGSGGGGV SSWGGASTWG GQGNGGASAW
960 970 980 990 1000
GGAGGGASAW GGQGTGATST WGGASAWGNK SSWGGASTWA SGGESNGAMS
1010 1020 1030 1040 1050
TWGGTGDRSA YGGASTWGGN NNNKSTRDGG ASAWGNQDDG NRSAWNNQGN
1060
KSNYGGNSTW GGH
Length:1,063
Mass (Da):115,650
Last modified:August 1, 1992 - v1
Checksum:iE4324DB6B1E4721A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M62882 Genomic DNA. Translation: AAA35085.1.
Z49810 Genomic DNA. Translation: CAA89942.1.
BK006946 Genomic DNA. Translation: DAA09888.1.
PIRiA40253.
RefSeqiNP_013703.1. NM_001182366.1.

Genome annotation databases

EnsemblFungiiYML010W; YML010W; YML010W.
GeneIDi854999.
KEGGisce:YML010W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M62882 Genomic DNA. Translation: AAA35085.1.
Z49810 Genomic DNA. Translation: CAA89942.1.
BK006946 Genomic DNA. Translation: DAA09888.1.
PIRiA40253.
RefSeqiNP_013703.1. NM_001182366.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EXUX-ray2.23A285-375[»]
4YTKX-ray1.09A382-511[»]
4YTLX-ray1.60A/B534-632[»]
ProteinModelPortaliP27692.
SMRiP27692. Positions 270-375, 382-508, 534-632, 800-847.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35159. 170 interactions.
DIPiDIP-6621N.
IntActiP27692. 89 interactions.
MINTiMINT-631921.

PTM databases

iPTMnetiP27692.

Proteomic databases

MaxQBiP27692.
PeptideAtlasiP27692.
PRIDEiP27692.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYML010W; YML010W; YML010W.
GeneIDi854999.
KEGGisce:YML010W.

Organism-specific databases

EuPathDBiFungiDB:YML010W.
SGDiS000004470. SPT5.

Phylogenomic databases

GeneTreeiENSGT00440000037640.
HOGENOMiHOG000189404.
InParanoidiP27692.
KOiK15172.
OMAiTQCRTIS.
OrthoDBiEOG77WWNF.

Enzyme and pathway databases

BioCyciYEAST:G3O-32614-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-72086. mRNA Capping.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

EvolutionaryTraceiP27692.
NextBioi978151.
PROiP27692.

Family and domain databases

InterProiIPR005824. KOW.
IPR006645. NGN_dom.
IPR024945. Spt5_C_dom.
IPR022581. Spt5_N.
IPR017071. TF_Spt5.
IPR005100. TF_Spt5_NGN-domain.
IPR008991. Translation_prot_SH3-like.
[Graphical view]
PfamiPF03439. Spt5-NGN. 1 hit.
PF11942. Spt5_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036945. Spt5. 1 hit.
SMARTiSM01104. CTD. 1 hit.
SM00739. KOW. 4 hits.
SM00738. NGN. 1 hit.
[Graphical view]
SUPFAMiSSF50104. SSF50104. 2 hits.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "SPT5, an essential gene important for normal transcription in Saccharomyces cerevisiae, encodes an acidic nuclear protein with a carboxy-terminal repeat."
    Swanson M.S., Malone E.A., Winston F.
    Mol. Cell. Biol. 11:3009-3019(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
    Strain: ATCC 204508 / S288c.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae."
    Hartzog G.A., Wada T., Handa H., Winston F.
    Genes Dev. 12:357-369(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN TRANSCRIPTION ELONGATION, IDENTIFICATION IN THE SPT4-SPT5 COMPLEX.
  5. "The Ras/PKA signaling pathway may control RNA polymerase II elongation via the Spt4p/Spt5p complex in Saccharomyces cerevisiae."
    Howard S.C., Hester A., Herman P.K.
    Genetics 165:1059-1070(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins."
    Lindstrom D.L., Squazzo S.L., Muster N., Burckin T.A., Wachter K.C., Emigh C.A., McCleery J.A., Yates J.R. III, Hartzog G.A.
    Mol. Cell. Biol. 23:1368-1378(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN TRANSCRIPTION ELONGATION AND MRNA PROCESSING.
  8. "Molecular evidence for a positive role of Spt4 in transcription elongation."
    Rondon A.G., Garcia-Rubio M., Gonzalez-Barrera S., Aguilera A.
    EMBO J. 22:612-620(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN TRANSCRIPTION ELONGATION.
  9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: ATCC 76625 / YPH499.
  10. "Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo."
    Mason P.B., Struhl K.
    Mol. Cell 17:831-840(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSIVITY.
  11. "Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing."
    Xiao Y., Yang Y.H., Burckin T.A., Shiue L., Hartzog G.A., Segal M.R.
    PLoS Comput. Biol. 1:276-288(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN ALTERNATIVE SPLICING.
  12. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-133 AND SER-136, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "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] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-35; SER-188 AND SER-219, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. "Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud."
    Shen Z., St-Denis A., Chartrand P.
    Genes Dev. 24:1914-1926(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SHE2.

Entry informationi

Entry nameiSPT5_YEAST
AccessioniPrimary (citable) accession number: P27692
Secondary accession number(s): D6VZG4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: May 11, 2016
This is version 159 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

It is phosphorylated in a PKA-dependent manner in vitro.
Present with 2340 molecules/cell in log phase SD medium.1 Publication

Caution

Was originally thought to be involved in the transcription initiation step.Curated

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 XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: 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.