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Protein

Transcription elongation factor SPT4

Gene

SPT4

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. The 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. Structural and functional component of the centromeric and heterochromatic loci linking chromatin structure with kinetochore function and gene silencing.7 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri7 – 2721C4-typeSequence analysisAdd
BLAST

GO - Molecular functioni

  • protein complex binding Source: SGD
  • rDNA binding Source: SGD
  • RNA polymerase II core binding Source: SGD
  • transcription factor activity, core RNA polymerase I binding Source: SGD
  • transcription factor activity, core RNA polymerase II binding Source: SGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • 7-methylguanosine mRNA capping Source: SGD
  • chromatin organization Source: SGD
  • chromatin silencing Source: SGD
  • chromosome segregation 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, DNA-templated 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

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-30778-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription elongation factor SPT4
Alternative name(s):
Chromatin elongation factor SPT4
Gene namesi
Name:SPT4
Ordered Locus Names:YGR063C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGR063C.
SGDiS000003295. SPT4.

Subcellular locationi

  • Nucleus 1 Publication
  • Chromosomecentromere 1 Publication

  • Note: Centromere and heterochromatin.

GO - Cellular componenti

  • chromosome, centromeric region Source: UniProtKB-SubCell
  • DSIF complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi10 – 101C → Y: Loss of function. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 102102Transcription elongation factor SPT4PRO_0000210338Add
BLAST

Proteomic databases

MaxQBiP32914.

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
HIR1P324792EBI-17928,EBI-8316
SPT5P276928EBI-17928,EBI-17937

GO - Molecular functioni

  • protein complex binding Source: SGD
  • RNA polymerase II core binding Source: SGD

Protein-protein interaction databases

BioGridi33308. 234 interactions.
DIPiDIP-2078N.
IntActiP32914. 11 interactions.
MINTiMINT-531590.

Structurei

Secondary structure

1
102
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 74Combined sources
Turni8 – 103Combined sources
Beta strandi12 – 154Combined sources
Helixi16 – 227Combined sources
Turni25 – 273Combined sources
Helixi28 – 347Combined sources
Helixi39 – 413Combined sources
Beta strandi42 – 443Combined sources
Beta strandi46 – 538Combined sources
Turni55 – 573Combined sources
Helixi59 – 635Combined sources
Beta strandi71 – 788Combined sources
Helixi84 – 874Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EXUX-ray2.23A1-99[»]
ProteinModelPortaliP32914.
SMRiP32914. Positions 3-99.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32914.

Family & Domainsi

Sequence similaritiesi

Belongs to the SPT4 family.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri7 – 2721C4-typeSequence analysisAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000018559.
HOGENOMiHOG000172685.
InParanoidiP32914.
KOiK15171.
OMAiACMLCGI.
OrthoDBiEOG7F51DX.

Family and domain databases

InterProiIPR029040. RPABC4/Spt4.
IPR009287. Spt4.
IPR016046. Spt4-like.
IPR022800. Spt4/RpoE2_Znf.
[Graphical view]
PANTHERiPTHR12882. PTHR12882. 1 hit.
PfamiPF06093. Spt4. 1 hit.
[Graphical view]
PIRSFiPIRSF025023. Spt4. 1 hit.
SMARTiSM01389. Spt4. 1 hit.
[Graphical view]
SUPFAMiSSF63393. SSF63393. 1 hit.

Sequencei

Sequence statusi: Complete.

P32914-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSERACMLC GIVQTTNEFN RDGCPNCQGI FEEAGVSTME CTSPSFEGLV
60 70 80 90 100
GMCKPTKSWV AKWLSVDHSI AGMYAIKVDG RLPAEVVELL PHYKPRDGSQ

VE
Length:102
Mass (Da):11,158
Last modified:October 1, 1993 - v1
Checksum:i59C164193ABA883B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M83672 Genomic DNA. Translation: AAA35084.1.
DQ115391 Genomic DNA. Translation: AAZ22476.1.
AM296426 Genomic DNA. Translation: CAL35887.1.
AM296427 Genomic DNA. Translation: CAL35886.1.
AM296428 Genomic DNA. Translation: CAL35885.1.
AM296429 Genomic DNA. Translation: CAL36074.1.
AM296430 Genomic DNA. Translation: CAL35884.1.
AM296431 Genomic DNA. Translation: CAL35883.1.
AM296432 Genomic DNA. Translation: CAL35882.1.
AM296433 Genomic DNA. Translation: CAL35881.1.
AM296434 Genomic DNA. Translation: CAL35880.1.
AM296435 Genomic DNA. Translation: CAL35879.1.
AM296436 Genomic DNA. Translation: CAL35878.1.
AM296437 Genomic DNA. Translation: CAL36075.1.
AM296438 Genomic DNA. Translation: CAL35877.1.
Z72848 Genomic DNA. Translation: CAA97065.1.
AY693090 Genomic DNA. Translation: AAT93109.1.
BK006941 Genomic DNA. Translation: DAA08159.1.
PIRiS31176.
RefSeqiNP_011577.3. NM_001181192.3.

Genome annotation databases

EnsemblFungiiYGR063C; YGR063C; YGR063C.
GeneIDi852955.
KEGGisce:YGR063C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M83672 Genomic DNA. Translation: AAA35084.1.
DQ115391 Genomic DNA. Translation: AAZ22476.1.
AM296426 Genomic DNA. Translation: CAL35887.1.
AM296427 Genomic DNA. Translation: CAL35886.1.
AM296428 Genomic DNA. Translation: CAL35885.1.
AM296429 Genomic DNA. Translation: CAL36074.1.
AM296430 Genomic DNA. Translation: CAL35884.1.
AM296431 Genomic DNA. Translation: CAL35883.1.
AM296432 Genomic DNA. Translation: CAL35882.1.
AM296433 Genomic DNA. Translation: CAL35881.1.
AM296434 Genomic DNA. Translation: CAL35880.1.
AM296435 Genomic DNA. Translation: CAL35879.1.
AM296436 Genomic DNA. Translation: CAL35878.1.
AM296437 Genomic DNA. Translation: CAL36075.1.
AM296438 Genomic DNA. Translation: CAL35877.1.
Z72848 Genomic DNA. Translation: CAA97065.1.
AY693090 Genomic DNA. Translation: AAT93109.1.
BK006941 Genomic DNA. Translation: DAA08159.1.
PIRiS31176.
RefSeqiNP_011577.3. NM_001181192.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EXUX-ray2.23A1-99[»]
ProteinModelPortaliP32914.
SMRiP32914. Positions 3-99.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33308. 234 interactions.
DIPiDIP-2078N.
IntActiP32914. 11 interactions.
MINTiMINT-531590.

Proteomic databases

MaxQBiP32914.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGR063C; YGR063C; YGR063C.
GeneIDi852955.
KEGGisce:YGR063C.

Organism-specific databases

EuPathDBiFungiDB:YGR063C.
SGDiS000003295. SPT4.

Phylogenomic databases

GeneTreeiENSGT00390000018559.
HOGENOMiHOG000172685.
InParanoidiP32914.
KOiK15171.
OMAiACMLCGI.
OrthoDBiEOG7F51DX.

Enzyme and pathway databases

BioCyciYEAST:G3O-30778-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.

Miscellaneous databases

EvolutionaryTraceiP32914.
PROiP32914.

Family and domain databases

InterProiIPR029040. RPABC4/Spt4.
IPR009287. Spt4.
IPR016046. Spt4-like.
IPR022800. Spt4/RpoE2_Znf.
[Graphical view]
PANTHERiPTHR12882. PTHR12882. 1 hit.
PfamiPF06093. Spt4. 1 hit.
[Graphical view]
PIRSFiPIRSF025023. Spt4. 1 hit.
SMARTiSM01389. Spt4. 1 hit.
[Graphical view]
SUPFAMiSSF63393. SSF63393. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular and genetic characterization of SPT4, a gene important for transcription initiation in Saccharomyces cerevisiae."
    Malone E.A., Fassler J.S., Winston F.
    Mol. Gen. Genet. 237:449-459(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    Strain: ATCC 204508 / S288c.
  2. "Molecular genetic dissection of a quantitative trait in yeast."
    Deutschbauer A.M., Davis R.W.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: SK1.
  3. "Sequence diversity, reproductive isolation and species concepts in Saccharomyces."
    Liti G., Barton D.B., Louis E.J.
    Genetics 174:839-850(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: DBVPG1135, DBVPG1373, DBVPG1378, DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6044, DBVPG6763, DBVPG6765, SK1, Y55 and YPS128.
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
    Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
    , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
    Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  7. "Faithful chromosome transmission requires Spt4p, a putative regulator of chromatin structure in Saccharomyces cerevisiae."
    Basrai M.A., Kingsbury J., Koshland D., Spencer F., Hieter P.
    Mol. Cell. Biol. 16:2838-2847(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-10.
  8. "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.
  9. "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.
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "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.
  12. "Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae."
    Crotti L.B., Basrai M.A.
    EMBO J. 23:1804-1814(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN CHROMATIN STRUCTURE, SUBCELLULAR LOCATION.
  13. "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.
  14. "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.
  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 nameiSPT4_YEAST
AccessioniPrimary (citable) accession number: P32914
Secondary accession number(s): D6VUJ8, Q0P6T7, Q45U23
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: July 6, 2016
This is version 147 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 4490 molecules/cell in log phase SD medium.1 Publication

Caution

Was originally thought to be involved in the transcription initiation step.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 VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: 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.