SPT4_YEAST
ID SPT4_YEAST Reviewed; 102 AA.
AC P32914; D6VUJ8; Q0P6T7; Q45U23;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 190.
DE RecName: Full=Transcription elongation factor SPT4;
DE AltName: Full=Chromatin elongation factor SPT4;
GN Name=SPT4; OrderedLocusNames=YGR063C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8483459; DOI=10.1007/bf00279450;
RA Malone E.A., Fassler J.S., Winston F.;
RT "Molecular and genetic characterization of SPT4, a gene important for
RT transcription initiation in Saccharomyces cerevisiae.";
RL Mol. Gen. Genet. 237:449-459(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=SK1;
RA Deutschbauer A.M., Davis R.W.;
RT "Molecular genetic dissection of a quantitative trait in yeast.";
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DBVPG1135, DBVPG1373, DBVPG1378, DBVPG1788, DBVPG1794, DBVPG1853,
RC DBVPG3051, DBVPG6044, DBVPG6763, DBVPG6765, SK1, Y55, and YPS128;
RX PubMed=16951060; DOI=10.1534/genetics.106.062166;
RA Liti G., Barton D.B., Louis E.J.;
RT "Sequence diversity, reproductive isolation and species concepts in
RT Saccharomyces.";
RL Genetics 174:839-850(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [7]
RP MUTAGENESIS OF CYS-10.
RX PubMed=8649393; DOI=10.1128/mcb.16.6.2838;
RA Basrai M.A., Kingsbury J., Koshland D., Spencer F., Hieter P.;
RT "Faithful chromosome transmission requires Spt4p, a putative regulator of
RT chromatin structure in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 16:2838-2847(1996).
RN [8]
RP FUNCTION IN TRANSCRIPTION ELONGATION, AND IDENTIFICATION IN THE SPT4-SPT5
RP COMPLEX.
RX PubMed=9450930; DOI=10.1101/gad.12.3.357;
RA Hartzog G.A., Wada T., Handa H., Winston F.;
RT "Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA
RT polymerase II in Saccharomyces cerevisiae.";
RL Genes Dev. 12:357-369(1998).
RN [9]
RP FUNCTION IN TRANSCRIPTION ELONGATION AND MRNA PROCESSING.
RX PubMed=12556496; DOI=10.1128/mcb.23.4.1368-1378.2003;
RA Lindstrom D.L., Squazzo S.L., Muster N., Burckin T.A., Wachter K.C.,
RA Emigh C.A., McCleery J.A., Yates J.R. III, Hartzog G.A.;
RT "Dual roles for Spt5 in pre-mRNA processing and transcription elongation
RT revealed by identification of Spt5-associated proteins.";
RL Mol. Cell. Biol. 23:1368-1378(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP FUNCTION IN TRANSCRIPTION ELONGATION.
RX PubMed=12554661; DOI=10.1093/emboj/cdg047;
RA Rondon A.G., Garcia-Rubio M., Gonzalez-Barrera S., Aguilera A.;
RT "Molecular evidence for a positive role of Spt4 in transcription
RT elongation.";
RL EMBO J. 22:612-620(2003).
RN [12]
RP FUNCTION IN CHROMATIN STRUCTURE, AND SUBCELLULAR LOCATION.
RX PubMed=15057281; DOI=10.1038/sj.emboj.7600161;
RA Crotti L.B., Basrai M.A.;
RT "Functional roles for evolutionarily conserved Spt4p at centromeres and
RT heterochromatin in Saccharomyces cerevisiae.";
RL EMBO J. 23:1804-1814(2004).
RN [13]
RP FUNCTION IN PROCESSIVITY.
RX PubMed=15780939; DOI=10.1016/j.molcel.2005.02.017;
RA Mason P.B., Struhl K.;
RT "Distinction and relationship between elongation rate and processivity of
RT RNA polymerase II in vivo.";
RL Mol. Cell 17:831-840(2005).
RN [14]
RP FUNCTION IN ALTERNATIVE SPLICING.
RX PubMed=16172632; DOI=10.1371/journal.pcbi.0010039;
RA Xiao Y., Yang Y.H., Burckin T.A., Shiue L., Hartzog G.A., Segal M.R.;
RT "Analysis of a splice array experiment elucidates roles of chromatin
RT elongation factor Spt4-5 in splicing.";
RL PLoS Comput. Biol. 1:276-288(2005).
RN [15]
RP SUBCELLULAR LOCATION.
RX PubMed=19683497; DOI=10.1016/j.molcel.2009.06.023;
RA Fillingham J., Kainth P., Lambert J.P., van Bakel H., Tsui K.,
RA Pena-Castillo L., Nislow C., Figeys D., Hughes T.R., Greenblatt J.,
RA Andrews B.J.;
RT "Two-color cell array screen reveals interdependent roles for histone
RT chaperones and a chromatin boundary regulator in histone gene repression.";
RL Mol. Cell 35:340-351(2009).
RN [16]
RP INTERACTION WITH SHE2.
RX PubMed=20713510; DOI=10.1101/gad.1937510;
RA Shen Z., St-Denis A., Chartrand P.;
RT "Cotranscriptional recruitment of She2p by RNA pol II elongation factor
RT Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud.";
RL Genes Dev. 24:1914-1926(2010).
CC -!- FUNCTION: The SPT4-SPT5 complex mediates both activation and inhibition
CC of transcription elongation, and plays a role in pre-mRNA processing.
CC The complex seems to be important for the stability of the RNA
CC polymerase II elongation machinery on the chromatin template but not
CC for the inherent ability of this machinery to translocate down the
CC gene. Structural and functional component of the centromeric and
CC heterochromatic loci linking chromatin structure with kinetochore
CC function and gene silencing. {ECO:0000269|PubMed:12554661,
CC ECO:0000269|PubMed:12556496, ECO:0000269|PubMed:15057281,
CC ECO:0000269|PubMed:15780939, ECO:0000269|PubMed:16172632,
CC ECO:0000269|PubMed:8483459, ECO:0000269|PubMed:9450930}.
CC -!- SUBUNIT: Component of the SPT4-SPT5 complex. Interacts with SHE2.
CC {ECO:0000269|PubMed:20713510, ECO:0000269|PubMed:9450930}.
CC -!- INTERACTION:
CC P32914; P32479: HIR1; NbExp=2; IntAct=EBI-17928, EBI-8316;
CC P32914; P40164: PSY2; NbExp=3; IntAct=EBI-17928, EBI-29107;
CC P32914; P27692: SPT5; NbExp=11; IntAct=EBI-17928, EBI-17937;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15057281}.
CC Chromosome, centromere {ECO:0000269|PubMed:15057281}. Chromosome
CC {ECO:0000269|PubMed:19683497}. Note=Centromere and heterochromatin
CC (PubMed:15057281). Associates with the coding region of HTA1
CC (PubMed:19683497). {ECO:0000269|PubMed:15057281,
CC ECO:0000269|PubMed:19683497}.
CC -!- MISCELLANEOUS: Present with 4490 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the SPT4 family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be involved in the transcription
CC initiation step. {ECO:0000305|PubMed:8483459}.
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DR EMBL; M83672; AAA35084.1; -; Genomic_DNA.
DR EMBL; DQ115391; AAZ22476.1; -; Genomic_DNA.
DR EMBL; AM296426; CAL35887.1; -; Genomic_DNA.
DR EMBL; AM296427; CAL35886.1; -; Genomic_DNA.
DR EMBL; AM296428; CAL35885.1; -; Genomic_DNA.
DR EMBL; AM296429; CAL36074.1; -; Genomic_DNA.
DR EMBL; AM296430; CAL35884.1; -; Genomic_DNA.
DR EMBL; AM296431; CAL35883.1; -; Genomic_DNA.
DR EMBL; AM296432; CAL35882.1; -; Genomic_DNA.
DR EMBL; AM296433; CAL35881.1; -; Genomic_DNA.
DR EMBL; AM296434; CAL35880.1; -; Genomic_DNA.
DR EMBL; AM296435; CAL35879.1; -; Genomic_DNA.
DR EMBL; AM296436; CAL35878.1; -; Genomic_DNA.
DR EMBL; AM296437; CAL36075.1; -; Genomic_DNA.
DR EMBL; AM296438; CAL35877.1; -; Genomic_DNA.
DR EMBL; Z72848; CAA97065.1; -; Genomic_DNA.
DR EMBL; AY693090; AAT93109.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08159.1; -; Genomic_DNA.
DR PIR; S31176; S31176.
DR RefSeq; NP_011577.3; NM_001181192.3.
DR PDB; 2EXU; X-ray; 2.23 A; A=1-99.
DR PDB; 7NKY; EM; 3.20 A; Y=1-102.
DR PDBsum; 2EXU; -.
DR PDBsum; 7NKY; -.
DR AlphaFoldDB; P32914; -.
DR SMR; P32914; -.
DR BioGRID; 33308; 246.
DR ComplexPortal; CPX-1661; SPT4-SPT5 transcription elongation factor complex.
DR DIP; DIP-2078N; -.
DR IntAct; P32914; 13.
DR MINT; P32914; -.
DR STRING; 4932.YGR063C; -.
DR iPTMnet; P32914; -.
DR MaxQB; P32914; -.
DR PaxDb; P32914; -.
DR PRIDE; P32914; -.
DR EnsemblFungi; YGR063C_mRNA; YGR063C; YGR063C.
DR GeneID; 852955; -.
DR KEGG; sce:YGR063C; -.
DR SGD; S000003295; SPT4.
DR VEuPathDB; FungiDB:YGR063C; -.
DR eggNOG; KOG3490; Eukaryota.
DR GeneTree; ENSGT00390000018559; -.
DR HOGENOM; CLU_138052_2_1_1; -.
DR InParanoid; P32914; -.
DR OMA; FDGMIAV; -.
DR BioCyc; YEAST:G3O-30778-MON; -.
DR Reactome; R-SCE-113418; Formation of the Early Elongation Complex.
DR Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-SCE-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-SCE-75955; RNA Polymerase II Transcription Elongation.
DR EvolutionaryTrace; P32914; -.
DR PRO; PR:P32914; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P32914; protein.
DR GO; GO:0032044; C:DSIF complex; IPI:SGD.
DR GO; GO:0000776; C:kinetochore; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IPI:ComplexPortal.
DR GO; GO:0044877; F:protein-containing complex binding; IDA:SGD.
DR GO; GO:0000182; F:rDNA binding; IDA:SGD.
DR GO; GO:0001181; F:RNA polymerase I general transcription initiation factor activity; IC:SGD.
DR GO; GO:0000993; F:RNA polymerase II complex binding; IDA:SGD.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006370; P:7-methylguanosine mRNA capping; IGI:SGD.
DR GO; GO:0006325; P:chromatin organization; IMP:SGD.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:SGD.
DR GO; GO:0008298; P:intracellular mRNA localization; IMP:SGD.
DR GO; GO:0006397; P:mRNA processing; IBA:GO_Central.
DR GO; GO:0010507; P:negative regulation of autophagy; IMP:SGD.
DR GO; GO:2001208; P:negative regulation of transcription elongation by RNA polymerase I; IGI:SGD.
DR GO; GO:2001209; P:positive regulation of transcription elongation from RNA polymerase I promoter; IMP:SGD.
DR GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IDA:SGD.
DR GO; GO:2000232; P:regulation of rRNA processing; IMP:SGD.
DR GO; GO:0034243; P:regulation of transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IDA:ComplexPortal.
DR GO; GO:0090262; P:regulation of transcription-coupled nucleotide-excision repair; IGI:SGD.
DR CDD; cd07973; Spt4; 1.
DR Gene3D; 3.30.40.210; -; 1.
DR InterPro; IPR029040; RPABC4/Spt4.
DR InterPro; IPR009287; Spt4.
DR InterPro; IPR022800; Spt4/RpoE2_Znf.
DR InterPro; IPR038510; Spt4_sf.
DR PANTHER; PTHR12882; PTHR12882; 1.
DR Pfam; PF06093; Spt4; 1.
DR PIRSF; PIRSF025023; Spt4; 1.
DR SMART; SM01389; Spt4; 1.
DR SUPFAM; SSF63393; SSF63393; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Centromere; Chromosome; Metal-binding; mRNA processing;
KW Nucleus; Reference proteome; Transcription; Zinc; Zinc-finger.
FT CHAIN 1..102
FT /note="Transcription elongation factor SPT4"
FT /id="PRO_0000210338"
FT ZN_FING 7..27
FT /note="C4-type"
FT /evidence="ECO:0000255"
FT MUTAGEN 10
FT /note="C->Y: Loss of function."
FT /evidence="ECO:0000269|PubMed:8649393"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:2EXU"
FT TURN 8..10
FT /evidence="ECO:0007829|PDB:2EXU"
FT STRAND 12..15
FT /evidence="ECO:0007829|PDB:2EXU"
FT HELIX 16..22
FT /evidence="ECO:0007829|PDB:2EXU"
FT TURN 25..27
FT /evidence="ECO:0007829|PDB:2EXU"
FT HELIX 28..34
FT /evidence="ECO:0007829|PDB:2EXU"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:2EXU"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:2EXU"
FT STRAND 46..53
FT /evidence="ECO:0007829|PDB:2EXU"
FT TURN 55..57
FT /evidence="ECO:0007829|PDB:2EXU"
FT HELIX 59..63
FT /evidence="ECO:0007829|PDB:2EXU"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:2EXU"
FT HELIX 84..87
FT /evidence="ECO:0007829|PDB:2EXU"
SQ SEQUENCE 102 AA; 11158 MW; 59C164193ABA883B CRC64;
MSSERACMLC GIVQTTNEFN RDGCPNCQGI FEEAGVSTME CTSPSFEGLV GMCKPTKSWV
AKWLSVDHSI AGMYAIKVDG RLPAEVVELL PHYKPRDGSQ VE
