NHP6A_YEAST
ID NHP6A_YEAST Reviewed; 93 AA.
AC P11632; D6W459;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1989, sequence version 1.
DT 03-AUG-2022, entry version 201.
DE RecName: Full=Non-histone chromosomal protein 6A;
GN Name=NHP6A; Synonyms=NHPA; OrderedLocusNames=YPR052C; ORFNames=YP9499.09C;
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].
RC STRAIN=DBY1091 / DKY1;
RX PubMed=2406250; DOI=10.1016/s0021-9258(19)39758-3;
RA Kolodrubetz D., Burgum A.;
RT "Duplicated NHP6 genes of Saccharomyces cerevisiae encode proteins
RT homologous to bovine high mobility group protein 1.";
RL J. Biol. Chem. 265:3234-3239(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1339437; DOI=10.1016/s0021-9258(19)88696-9;
RA Tercero J.C., Riles L.E., Wickner R.B.;
RT "Localized mutagenesis and evidence for post-transcriptional regulation of
RT MAK3. A putative N-acetyltransferase required for double-stranded RNA virus
RT propagation in Saccharomyces cerevisiae.";
RL J. Biol. Chem. 267:20270-20276(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [4]
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 [5]
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 [6]
RP FUNCTION.
RX PubMed=7721780; DOI=10.1074/jbc.270.15.8744;
RA Paull T.T., Johnson R.C.;
RT "DNA looping by Saccharomyces cerevisiae high mobility group proteins
RT NHP6A/B. Consequences for nucleoprotein complex assembly and chromatin
RT condensation.";
RL J. Biol. Chem. 270:8744-8754(1995).
RN [7]
RP FUNCTION.
RX PubMed=8946917; DOI=10.1101/gad.10.21.2769;
RA Paull T.T., Carey M., Johnson R.C.;
RT "Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional
RT activation in vivo and assembly of preinitiation complexes in vitro.";
RL Genes Dev. 10:2769-2781(1996).
RN [8]
RP DNA-BINDING, AND MUTAGENESIS OF PRO-18; PRO-21; TYR-28; MET-29; PHE-30 AND
RP PHE-31.
RX PubMed=9468494; DOI=10.1074/jbc.273.8.4424;
RA Yen Y.-M., Wong B., Johnson R.C.;
RT "Determinants of DNA binding and bending by the Saccharomyces cerevisiae
RT high mobility group protein NHP6A that are important for its biological
RT activities. Role of the unique N terminus and putative intercalating
RT methionine.";
RL J. Biol. Chem. 273:4424-4435(1998).
RN [9]
RP FUNCTION.
RX PubMed=11118215; DOI=10.1093/emboj/19.24.6804;
RA Moreira J.M.A., Holmberg S.;
RT "Chromatin-mediated transcriptional regulation by the yeast architectural
RT factors NHP6A and NHP6B.";
RL EMBO J. 19:6804-6813(2000).
RN [10]
RP ASSOCIATION WITH THE SPT16-POB3 DIMER AND NUCLEOSOMES, AND FUNCTION OF THE
RP FACT COMPLEX.
RX PubMed=11432837; DOI=10.1093/emboj/20.13.3506;
RA Formosa T., Eriksson P., Wittmeyer J., Ginn J., Yu Y., Stillman D.J.;
RT "Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding
RT factor SPN.";
RL EMBO J. 20:3506-3517(2001).
RN [11]
RP FUNCTION.
RX PubMed=11239460; DOI=10.1016/s1097-2765(01)00179-4;
RA Kruppa M., Moir R.D., Kolodrubetz D., Willis I.M.;
RT "Nhp6, an HMG1 protein, functions in SNR6 transcription by RNA polymerase
RT III in S. cerevisiae.";
RL Mol. Cell 7:309-318(2001).
RN [12]
RP ERRATUM OF PUBMED:11239460.
RA Kruppa M., Moir R.D., Kolodrubetz D., Willis I.M.;
RL Mol. Cell 8:727-727(2001).
RN [13]
RP FUNCTION.
RX PubMed=11287614; DOI=10.1128/mcb.21.9.3096-3104.2001;
RA Lopez S., Livingstone-Zatchej M., Jourdain S., Thoma F., Sentenac A.,
RA Marsolier M.-C.;
RT "High-mobility-group proteins NHP6A and NHP6B participate in activation of
RT the RNA polymerase III SNR6 gene.";
RL Mol. Cell. Biol. 21:3096-3104(2001).
RN [14]
RP ASSOCIATION WITH THE SPT16-POB3 DIMER.
RX PubMed=11313475; DOI=10.1128/mcb.21.10.3491-3502.2001;
RA Brewster N.K., Johnston G.C., Singer R.A.;
RT "A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins
RT modulates transcription.";
RL Mol. Cell. Biol. 21:3491-3502(2001).
RN [15]
RP SUBCELLULAR LOCATION.
RX PubMed=11422939; DOI=10.1034/j.1600-0854.2001.20703.x;
RA Yen Y.-M., Roberts P.M., Johnson R.C.;
RT "Nuclear localization of the Saccharomyces cerevisiae HMG protein NHP6A
RT occurs by a Ran-independent nonclassical pathway.";
RL Traffic 2:449-464(2001).
RN [16]
RP FUNCTION.
RX PubMed=12952948; DOI=10.1074/jbc.m307291200;
RA Ruone S., Rhoades A.R., Formosa T.;
RT "Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT
RT complexes and to reorganize nucleosomes.";
RL J. Biol. Chem. 278:45288-45295(2003).
RN [17]
RP FUNCTION OF THE FACT COMPLEX.
RX PubMed=14585989; DOI=10.1128/mcb.23.22.8323-8333.2003;
RA Mason P.B., Struhl K.;
RT "The FACT complex travels with elongating RNA polymerase II and is
RT important for the fidelity of transcriptional initiation in vivo.";
RL Mol. Cell. Biol. 23:8323-8333(2003).
RN [18]
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 [19]
RP DNA-BINDING.
RX PubMed=15504049; DOI=10.1021/bi048428o;
RA Skoko D., Wong B., Johnson R.C., Marko J.F.;
RT "Micromechanical analysis of the binding of DNA-bending proteins HMGB1,
RT NHP6A, and HU reveals their ability to form highly stable DNA-protein
RT complexes.";
RL Biochemistry 43:13867-13874(2004).
RN [20]
RP SUBCELLULAR LOCATION.
RX PubMed=14739930; DOI=10.1038/sj.emboj.7600053;
RA Kim M., Ahn S.-H., Krogan N.J., Greenblatt J.F., Buratowski S.;
RT "Transitions in RNA polymerase II elongation complexes at the 3' ends of
RT genes.";
RL EMBO J. 23:354-364(2004).
RN [21]
RP FUNCTION OF THE FACT COMPLEX.
RX PubMed=15082784; DOI=10.1128/mcb.24.9.3907-3917.2004;
RA Rhoades A.R., Ruone S., Formosa T.;
RT "Structural features of nucleosomes reorganized by yeast FACT and its HMG
RT box component, Nhp6.";
RL Mol. Cell. Biol. 24:3907-3917(2004).
RN [22]
RP FUNCTION OF THE FACT COMPLEX.
RX PubMed=15987999; DOI=10.1128/mcb.25.14.5812-5822.2005;
RA Biswas D., Yu Y., Prall M., Formosa T., Stillman D.J.;
RT "The yeast FACT complex has a role in transcriptional initiation.";
RL Mol. Cell. Biol. 25:5812-5822(2005).
RN [23]
RP FUNCTION.
RX PubMed=16407207; DOI=10.1074/jbc.m512810200;
RA Kassavetis G.A., Steiner D.F.;
RT "Nhp6 is a transcriptional initiation fidelity factor for RNA polymerase
RT III transcription in vitro and in vivo.";
RL J. Biol. Chem. 281:7445-7451(2006).
RN [24]
RP STRUCTURE BY NMR IN COMPLEX WITH DNA.
RX PubMed=10228169; DOI=10.1093/emboj/18.9.2563;
RA Allain F.H.-T., Yen Y.-M., Masse J.E., Schultze P., Dieckmann T.,
RA Johnson R.C., Feigon J.;
RT "Solution structure of the HMG protein NHP6A and its interaction with DNA
RT reveals the structural determinants for non-sequence-specific binding.";
RL EMBO J. 18:2563-2579(1999).
RN [25]
RP STRUCTURE BY NMR IN COMPLEX WITH DNA.
RX PubMed=12381320; DOI=10.1016/s0022-2836(02)00938-5;
RA Masse J.E., Wong B., Yen Y.-M., Allain F.H.-T., Johnson R.C., Feigon J.;
RT "The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA
RT and protein conformational changes upon binding.";
RL J. Mol. Biol. 323:263-284(2002).
CC -!- FUNCTION: DNA-binding protein that induces severe bending of DNA.
CC Required for DNA-binding by the FACT complex, a general chromatin
CC factor that acts to reorganize nucleosomes. The FACT complex is
CC involved in multiple processes that require DNA as a template such as
CC mRNA elongation, DNA replication and DNA repair. Also augments the
CC fidelity of transcription by RNA polymerase III independently of any
CC role in the FACT complex. Required for transcriptional initiation
CC fidelity of some but not all tRNA genes. Seems to be functionally
CC redundant with NHP6B. {ECO:0000269|PubMed:11118215,
CC ECO:0000269|PubMed:11239460, ECO:0000269|PubMed:11287614,
CC ECO:0000269|PubMed:11432837, ECO:0000269|PubMed:12952948,
CC ECO:0000269|PubMed:14585989, ECO:0000269|PubMed:15082784,
CC ECO:0000269|PubMed:15987999, ECO:0000269|PubMed:16407207,
CC ECO:0000269|PubMed:7721780, ECO:0000269|PubMed:8946917}.
CC -!- SUBUNIT: Weakly associates with the stable SPT16-POB3 heterodimer to
CC form the FACT (yFACT or SNP) complex, which is associated with
CC nucleosomes. Multiple molecules of NHP6 (NHP6A and/or NHP6B) are
CC required to recruit the SPT16-POB3 heterodimer to DNA.
CC {ECO:0000269|PubMed:10228169, ECO:0000269|PubMed:12381320}.
CC -!- INTERACTION:
CC P11632; P32597: STH1; NbExp=3; IntAct=EBI-12019, EBI-18410;
CC -!- SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Colocalizes with both
CC RNA polymerase II and some regions that are not transcribed on
CC chromatin.
CC -!- MISCELLANEOUS: Present with 3870 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the NHP6 family. {ECO:0000305}.
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DR EMBL; X15317; CAA33377.1; -; Genomic_DNA.
DR EMBL; M95912; AAA34754.1; -; Genomic_RNA.
DR EMBL; Z49219; CAA89171.1; -; Genomic_DNA.
DR EMBL; Z71255; CAA94998.1; -; Genomic_DNA.
DR EMBL; AY693230; AAT93249.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11475.1; -; Genomic_DNA.
DR PIR; A35072; A35072.
DR RefSeq; NP_015377.1; NM_001184149.1.
DR PDB; 1CG7; NMR; -; A=1-93.
DR PDB; 1J5N; NMR; -; A=1-93.
DR PDB; 1LWM; NMR; -; A=1-93.
DR PDBsum; 1CG7; -.
DR PDBsum; 1J5N; -.
DR PDBsum; 1LWM; -.
DR AlphaFoldDB; P11632; -.
DR BMRB; P11632; -.
DR SMR; P11632; -.
DR BioGRID; 36227; 184.
DR IntAct; P11632; 62.
DR MINT; P11632; -.
DR STRING; 4932.YPR052C; -.
DR iPTMnet; P11632; -.
DR MaxQB; P11632; -.
DR PaxDb; P11632; -.
DR PRIDE; P11632; -.
DR TopDownProteomics; P11632; -.
DR EnsemblFungi; YPR052C_mRNA; YPR052C; YPR052C.
DR GeneID; 856165; -.
DR KEGG; sce:YPR052C; -.
DR SGD; S000006256; NHP6A.
DR VEuPathDB; FungiDB:YPR052C; -.
DR eggNOG; KOG0381; Eukaryota.
DR GeneTree; ENSGT00940000176448; -.
DR HOGENOM; CLU_082854_10_3_1; -.
DR InParanoid; P11632; -.
DR OMA; QKAPYEA; -.
DR BioCyc; YEAST:G3O-34205-MON; -.
DR ChiTaRS; NHP6A; yeast.
DR EvolutionaryTrace; P11632; -.
DR PRO; PR:P11632; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; P11632; protein.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0032993; C:protein-DNA complex; IMP:CAFA.
DR GO; GO:0008301; F:DNA binding, bending; IDA:SGD.
DR GO; GO:0032407; F:MutSalpha complex binding; IDA:SGD.
DR GO; GO:0031491; F:nucleosome binding; IDA:SGD.
DR GO; GO:0006338; P:chromatin remodeling; IGI:SGD.
DR GO; GO:0034724; P:DNA replication-independent chromatin organization; IDA:SGD.
DR GO; GO:0001195; P:maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter; IDA:SGD.
DR GO; GO:0006298; P:mismatch repair; IC:SGD.
DR GO; GO:0043392; P:negative regulation of DNA binding; IDA:SGD.
DR GO; GO:0065004; P:protein-DNA complex assembly; IMP:CAFA.
DR GO; GO:0051123; P:RNA polymerase II preinitiation complex assembly; IDA:SGD.
DR GO; GO:0070898; P:RNA polymerase III preinitiation complex assembly; IDA:SGD.
DR DisProt; DP00432; -.
DR Gene3D; 1.10.30.10; -; 1.
DR IDEAL; IID50069; -.
DR InterPro; IPR009071; HMG_box_dom.
DR InterPro; IPR036910; HMG_box_dom_sf.
DR Pfam; PF00505; HMG_box; 1.
DR SMART; SM00398; HMG; 1.
DR SUPFAM; SSF47095; SSF47095; 1.
DR PROSITE; PS50118; HMG_BOX_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromosome; DNA damage; DNA repair; DNA-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..93
FT /note="Non-histone chromosomal protein 6A"
FT /id="PRO_0000048565"
FT DNA_BIND 21..89
FT /note="HMG box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 69..93
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 69..86
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 18
FT /note="P->A: Does not affect affinity for DNA."
FT /evidence="ECO:0000269|PubMed:9468494"
FT MUTAGEN 21
FT /note="P->A: Shows a 4-fold reduced affinity for DNA."
FT /evidence="ECO:0000269|PubMed:9468494"
FT MUTAGEN 28
FT /note="Y->D: Shows a strongly reduced affinity for linear
FT and circular DNA."
FT /evidence="ECO:0000269|PubMed:9468494"
FT MUTAGEN 29
FT /note="M->A,D: Unable to form 75 bp microcircles."
FT /evidence="ECO:0000269|PubMed:9468494"
FT MUTAGEN 30
FT /note="F->V: Does not affect affinity for DNA."
FT /evidence="ECO:0000269|PubMed:9468494"
FT MUTAGEN 31
FT /note="F->D: Shows a strongly reduced affinity for linear
FT and circular DNA."
FT /evidence="ECO:0000269|PubMed:9468494"
FT STRAND 17..19
FT /evidence="ECO:0007829|PDB:1J5N"
FT HELIX 27..35
FT /evidence="ECO:0007829|PDB:1CG7"
FT TURN 38..42
FT /evidence="ECO:0007829|PDB:1CG7"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:1CG7"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:1CG7"
FT HELIX 55..60
FT /evidence="ECO:0007829|PDB:1CG7"
FT HELIX 63..74
FT /evidence="ECO:0007829|PDB:1CG7"
FT HELIX 77..80
FT /evidence="ECO:0007829|PDB:1CG7"
FT HELIX 83..91
FT /evidence="ECO:0007829|PDB:1CG7"
SQ SEQUENCE 93 AA; 10802 MW; A227296A12D440D8 CRC64;
MVTPREPKKR TTRKKKDPNA PKRALSAYMF FANENRDIVR SENPDITFGQ VGKKLGEKWK
ALTPEEKQPY EAKAQADKKR YESEKELYNA TLA
