Reviewed, UniProtKB/Swiss-Prot P32558 (SPT16_YEAST)

Names and origin

Protein names

Recommended name:
    FACT complex subunit SPT16
Alternative name(s):
    Facilitates chromatin transcription complex subunit SPT16
    Suppressor of Ty protein 16
    Cell division control protein 68

Gene names

Name:	SPT16
Synonyms:	CDC68, SSF1
Ordered Locus Names:	YGL207W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	1035 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishement of the nucleosome following the passage of RNA polymerase II. Transcription elongation is promoted by the repression of transcription initiation from cryptic sites. Also acts in establishing transcription initiation complexes and promotes SPT15/TBP-binding to a TATA box. Together with replication factor-A protein (RPA), FACT may play a role in nucleosome deposition during DNA replication.
Subunit structure	Forms a stable heterodimer with POB3. The SPT16-POB3 dimer weakly associates with multiple molecules of NHP6 (NHP6A or NHP6B) to form the FACT (yFACT or SNP) complex. The FACT complex interacts with the CK2 (casein kinase II) complex subunits CKA1, CKA2, CKB1 and CKB2 and the components of the transcription machinery CHD1, CTR9, PAF1 and CDC73. The FACT complex interacts with the PAF1 complex. SPT16 interacts with SAS3 and POL1.
Subcellular location	Nucleus. Note= Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci.
Miscellaneous	Present with 18500 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase M24 family. SPT16 subfamily.
Caution	Although related to the peptidase M24 family, this protein lacks conserved active site residues suggesting that it may lack peptidase activity.

Ontologies

Keywords
Biological process	DNA damage DNA repair DNA replication Transcription Transcription regulation
Cellular component	Chromosomal protein Nucleus
Domain	Coiled coil
Molecular function	Activator Repressor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	RNA elongation from RNA polymerase II promoter Ref.15 Inferred from physical interaction. Source: SGD nucleosome assembly Ref.17 Ref.23 Inferred from direct assay. Source: SGD transcription initiation from RNA polymerase II promoter Ref.24 Inferred from direct assay. Source: SGD
Cellular component	FACT complex Ref.11 Inferred from genetic interaction. Source: SGD nuclear chromatin Ref.9 Inferred from direct assay. Source: SGD
Molecular function	RNA polymerase II transcription elongation factor activity Ref.15 Inferred from physical interaction. Source: SGD protein binding Ref.15 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
POB3	Q04636	1	EBI-4334,EBI-27863
SAS3	P34218	1	EBI-4334,EBI-16484

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view
Molecule processing
	Chain	1 – 1035	1035	FACT complex subunit SPT16
Regions
	Coiled coil	208 – 234	27	Potential
	Coiled coil	636 – 666	31	Potential
	Coiled coil	959 – 983	25	Potential
	Compositional bias	958 – 1021	64	Asp/Glu-rich (acidic)
Amino acid modifications
	Modified residue	235	1	Phosphoserine
	Modified residue	460	1	Phosphoserine
	Modified residue	526	1	Phosphoserine
	Modified residue	542	1	Phosphoserine
	Modified residue	598	1	Phosphoserine
	Modified residue	601	1	Phosphoserine
	Modified residue	602	1	Phosphoserine
	Modified residue	765	1	Phosphoserine
	Modified residue	1011	1	Phosphoserine
Experimental info
	Mutagenesis	565	1	P → S in spt16-4; induces a spt phenotype characterized by depletion of many mRNAs; when associated with L-570
	Mutagenesis	570	1	P → L in spt16-4; induces a spt phenotype characterized by depletion of many mRNAs; when associated with S-565
	Mutagenesis	836	1	G → D in cdc68-1; induces a spt phenotype characterized by depletion of many mRNAs
	Mutagenesis	848 – 850	3	TTD → IIY in spt16-7; induces a spt phenotype characterized by depletion of many mRNAs
	Mutagenesis	920	1	P → L in spt16-6; induces a spt phenotype characterized by depletion of many mRNAs

Sequences

	Sequence		Length	Mass (Da)
	P32558-1 [UniParc]. Last modified October 1, 1993. Version 1. Checksum: 4F01C772E299E2E6	FASTA	1,035	118,630
	10 20 30 40 50 60 MEELNIDFDV FKKRIELLYS KYNEFEGSPN SLLFVLGSSN AENPYQKTTI LHNWLLSYEF 70 80 90 100 110 120 PATLIALVPG KVIIITSSAK AKHLQKAIDL FKDPESKITL ELWQRNNKEP ELNKKLFDDV 130 140 150 160 170 180 IALINSAGKT VGIPEKDSYQ GKFMTEWNPV WEAAVKENEF NVIDISLGLS KVWEVKDVNE 190 200 210 220 230 240 QAFLSVSSKG SDKFMDLLSN EMVRAVDEEL KITNAKLSDK IENKIDDVKF LKQLSPDLSA 250 260 270 280 290 300 LCPPNYKFNF DLLDWTYSPI IQSGKKFDLR VSARSTNDQL YGNGCILASC GIRYNNYCSN 310 320 330 340 350 360 ITRTFLIDPS EEMANNYDFL LTLQKEIVTN ILKPGRTPKE VYESVIEYIE KTKPELVPNF 370 380 390 400 410 420 TKNIGSLIGL EFRDSNFILN VKNDYRKIQR GDCFNISFGF NNLKDSQSAN NYALQLADTV 430 440 450 460 470 480 QIPLDETEPP RFLTNYTKAK SQISFYFNNE EEDNNKKKSS PATKVPSKPD RNSKILRTKL 490 500 510 520 530 540 RGEARGGAED AQKEQIRKEN QKKLHEKLEK NGLLRFSAAD ANGPDSEPRQ YFKKYESYVR 550 560 570 580 590 600 DSQLPTNIRD LRIHVDWKSQ TIILPIYGRP VPFHINSYKN GSKNEEGEYT YLRLNFNSPG 610 620 630 640 650 660 SSGGISKKVE ELPYEESADN QFVRSITLRS KDGDRMSETF KQIADLKKEA TKREQERKAL 670 680 690 700 710 720 ADVVQQDKLI ENKTGRTKRL DQIFVRPNPD TKRVPSTVFI HENGIRFQSP LRTDSRIDIL 730 740 750 760 770 780 FSNIKNLIFQ SCKGELIVVI HIHLKNPILM GKKKIQDVQF YREASDMSVD ETGGGRRGQS 790 800 810 820 830 840 RFRRYGDEDE LEQEQEERRK RAALDKEFKY FADAIAEASN GLLTVENTFR DLGFQGVPNR 850 860 870 880 890 900 SAVFCMPTTD CLVQLIEPPF LVINLEEVEI CILERVQFGL KNFDMVFVYK DFNKPVTHIN 910 920 930 940 950 960 TVPIESLDFL KQWLTDMDIP YTVSTINLNW ATIMKSLQDD PYQFFLDGGW NFLATGSDDE 970 980 990 1000 1010 1020 ASDESEEEVS EYEASEDDVS DESAFSEDEE GSEVDDDISG DESEDYTGDE SEEGEDWDEL 1030 EKKAARADRG ANFRD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"CDC68, a yeast gene that affects regulation of cell proliferation and transcription, encodes a protein with a highly acidic carboxyl terminus." Rowley A., Singer R.A., Johnston G.C. Mol. Cell. Biol. 11:5718-5726(1991) [PubMed: 1833637] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Mutations in SPT16/CDC68 suppress cis- and trans-acting mutations that affect promoter function in Saccharomyces cerevisiae." Malone E.A., Clark C.D., Chiang A., Winston F. Mol. Cell. Biol. 11:5710-5717(1991) [PubMed: 1922073] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Analysis of 21.7 kb DNA sequence from the left arm of chromosome VII reveals 11 open reading frames: two correspond to new genes." Feuermann M., Simeonava L., Souciet J.-L., Potier S. Yeast 13:475-477(1997) [PubMed: 9153757] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	"Organization of the yeast URA2 gene: identification of a defective dihydroorotase-like domain in the multifunctional carbamoylphosphate synthetase-aspartate transcarbamylase complex." Souciet J.-L., Nagy M., le Gouar M., Lacroute F., Potier S. Gene 79:59-70(1989) [PubMed: 2570735] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-158. Strain: ATCC 28383 / FL100 / VTT C-80102.
[6]	"The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein." Wittmeyer J., Formosa T. Mol. Cell. Biol. 17:4178-4190(1997) [PubMed: 9199353] [Abstract] Cited for: INTERACTION WITH POL1.
[7]	"The yeast protein complex containing cdc68 and pob3 mediates core-promoter repression through the cdc68 N-terminal domain." Evans D.R.H., Brewster N.K., Xu Q., Rowley A., Altheim B.A., Johnston G.C., Singer R.A. Genetics 150:1393-1405(1998) [PubMed: 9832518] [Abstract] Cited for: INTERACTION WITH POB3, MUTAGENESIS OF GLY-836.
[8]	"Characterization of the CP complex, an abundant dimer of Cdc68 and Pob3 proteins that regulates yeast transcriptional activation and chromatin repression." Brewster N.K., Johnston G.C., Singer R.A. J. Biol. Chem. 273:21972-21979(1998) [PubMed: 9705338] [Abstract] Cited for: INTERACTION WITH POB3.
[9]	"Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha." Wittmeyer J., Joss L., Formosa T. Biochemistry 38:8961-8971(1999) [PubMed: 10413469] [Abstract] Cited for: FUNCTION, INTERACTION WITH POB3, SUBCELLULAR LOCATION.
[10]	"The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex." John S., Howe L., Tafrov S.T., Grant P.A., Sternglanz R., Workman J.L. Genes Dev. 14:1196-1208(2000) [PubMed: 10817755] [Abstract] Cited for: INTERACTION WITH SAS3.
[11]	"Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN." Formosa T., Eriksson P., Wittmeyer J., Ginn J., Yu Y., Stillman D.J. EMBO J. 20:3506-3517(2001) [PubMed: 11432837] [Abstract] Cited for: ASSOCIATION OF THE SPT16-POB3 DIMER WITH NHP6A/B AND NUCLEOSOMES, FUNCTION OF THE FACT COMPLEX, MUTAGENESIS OF PRO-565; PRO-570; 848-THR--ASP-850 AND PRO-920.
[12]	"A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins modulates transcription." Brewster N.K., Johnston G.C., Singer R.A. Mol. Cell. Biol. 21:3491-3502(2001) [PubMed: 11313475] [Abstract] Cited for: ASSOCIATION OF THE SPT16-POB3 DIMER WITH NHP6A/B.
[13]	"The Paf1 complex physically and functionally associates with transcription elongation factors in vivo." Squazzo S.L., Costa P.J., Lindstrom D.L., Kumer K.E., Simic R., Jennings J.L., Link A.J., Arndt K.M., Hartzog G.A. EMBO J. 21:1764-1774(2002) [PubMed: 11927560] [Abstract] Cited for: INTERACTION WITH PAF1 COMPLEX.
[14]	"Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: polymerase passage may degrade chromatin structure." Formosa T., Ruone S., Adams M.D., Olsen A.E., Eriksson P., Yu Y., Rhoades A.R., Kaufman P.D., Stillman D.J. Genetics 162:1557-1571(2002) [PubMed: 12524332] [Abstract] Cited for: FUNCTION OF THE FACT COMPLEX.
[15]	"RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach." Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A., Shilatifard A., Buratowski S., Greenblatt J.F. Mol. Cell. Biol. 22:6979-6992(2002) [PubMed: 12242279] [Abstract] Cited for: INTERACTION WITH CHD1; CTR9; PAF1; CDC73; CKA1; CKA2; CKB1; CKB2 AND HISTONES.
[16]	"Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes." Simic R., Lindstrom D.L., Tran H.G., Roinick K.L., Costa P.J., Johnson A.D., Hartzog G.A., Arndt K.M. EMBO J. 22:1846-1856(2003) [PubMed: 12682017] [Abstract] Cited for: INTERACTION WITH CHD1.
[17]	"Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes." Ruone S., Rhoades A.R., Formosa T. J. Biol. Chem. 278:45288-45295(2003) [PubMed: 12952948] [Abstract] Cited for: ASSOCIATION OF THE SPT16-POB3 DIMER WITH NHP6A/B.
[18]	"The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo." Mason P.B., Struhl K. Mol. Cell. Biol. 23:8323-8333(2003) [PubMed: 14585989] [Abstract] Cited for: FUNCTION OF THE FACT COMPLEX, SUBCELLULAR LOCATION.
[19]	Erratum Mason P.B., Struhl K. Mol. Cell. Biol. 24:6536-6536(2004)
[20]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[21]	"Transcription elongation factors repress transcription initiation from cryptic sites." Kaplan C.D., Laprade L., Winston F. Science 301:1096-1099(2003) [PubMed: 12934008] [Abstract] Cited for: FUNCTION OF THE FACT COMPLEX.
[22]	"Transitions in RNA polymerase II elongation complexes at the 3' ends of genes." Kim M., Ahn S.-H., Krogan N.J., Greenblatt J.F., Buratowski S. EMBO J. 23:354-364(2004) [PubMed: 14739930] [Abstract] Cited for: SUBCELLULAR LOCATION.
[23]	"Structural features of nucleosomes reorganized by yeast FACT and its HMG box component, Nhp6." Rhoades A.R., Ruone S., Formosa T. Mol. Cell. Biol. 24:3907-3917(2004) [PubMed: 15082784] [Abstract] Cited for: FUNCTION OF THE FACT COMPLEX.
[24]	"The yeast FACT complex has a role in transcriptional initiation." Biswas D., Yu Y., Prall M., Formosa T., Stillman D.J. Mol. Cell. Biol. 25:5812-5822(2005) [PubMed: 15987999] [Abstract] Cited for: FUNCTION OF THE FACT COMPLEX.
[25]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-460, MASS SPECTROMETRY.
[26]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-235; SER-460; SER-526; SER-542; SER-598; SER-601; SER-602; SER-765 AND SER-1011, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M73533 Genomic DNA. No translation available.
Z72729 Genomic DNA. Translation: CAA96920.1.
M27174 Genomic DNA. No translation available.

PIR

S18512.

RefSeq

NP_011308.1.

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3BIP	X-ray	1.94	A/B	1-465	[»]
3BIQ	X-ray	1.73	A	1-465	[»]
3BIT	X-ray	1.90	A/B	1-451	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:2546N.

IntAct

P32558.

Proteomic databases

PeptideAtlas

P32558.

Genome annotation databases

Ensembl

YGL207W. Saccharomyces cerevisiae. [Contig view]

GeneID

852665.

GenomeReviews

Gene locus YGL207W in contig Y13135_GR.

KEGG

sce:YGL207W.

NMPDR

fig|4932.3.peg.2411.

Organism-specific databases

CYGD

YGL207w.

SGD

S000003175. SPT16.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P32558.

Gene expression databases

ArrayExpress

P32558.

GermOnline

YGL207W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR013719. DUF1747_euk.
IPR013953. FACT_Spt16p.
IPR000994. Peptidase_M24_cat_core.
[Graphical view]

Gene3D

G3DSA:3.90.230.10. Peptidase_M24_cat_core. 1 hit.

Pfam

PF08512. Rtt106. 1 hit.
PF08644. SPT16. 1 hit.
[Graphical view]

ProDom

P32558.
[Graphical view] [Entries sharing at least one domain]

BLOCKS

Search...

Other Resources

LinkHub

P32558.

ProtoNet

Search...

Entry information

Entry name

SPT16_YEAST

Accession

Primary (citable) accession number: P32558

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1993
Last modified:	September 2, 2008
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)