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Protein

Non-histone chromosomal protein 6A

Gene

NHP6A

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

DNA-binding protein that induces severe bending of DNA. Required for DNA-binding by 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. Also augments the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. Required for transcriptional initiation fidelity of some but not all tRNA genes. Seems to be functionally redundant with NHP6B.11 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi21 – 8969HMG boxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding, bending Source: SGD
  • nucleosome binding Source: SGD

GO - Biological processi

  • chromatin remodeling Source: SGD
  • DNA replication-independent nucleosome organization Source: SGD
  • maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter Source: SGD
  • mismatch repair Source: SGD
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • RNA polymerase III transcriptional preinitiation complex assembly Source: SGD
  • RNA polymerase II transcriptional preinitiation complex assembly Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-34205-MONOMER.
ReactomeiR-SCE-211227. Activation of DNA fragmentation factor.

Names & Taxonomyi

Protein namesi
Recommended name:
Non-histone chromosomal protein 6A
Gene namesi
Name:NHP6A
Synonyms:NHPA
Ordered Locus Names:YPR052C
ORF Names:YP9499.09C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPR052C.
SGDiS000006256. NHP6A.

Subcellular locationi

  • Nucleus
  • Chromosome

  • Note: Colocalizes with both RNA polymerase II and some regions that are not transcribed on chromatin.

GO - Cellular componenti

  • chromosome Source: UniProtKB-SubCell
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi18 – 181P → A: Does not affect affinity for DNA. 1 Publication
Mutagenesisi21 – 211P → A: Shows a 4-fold reduced affinity for DNA. 1 Publication
Mutagenesisi28 – 281Y → D: Shows a strongly reduced affinity for linear and circular DNA. 1 Publication
Mutagenesisi29 – 291M → A or D: Unable to form 75 bp microcircles. 1 Publication
Mutagenesisi30 – 301F → V: Does not affect affinity for DNA. 1 Publication
Mutagenesisi31 – 311F → D: Shows a strongly reduced affinity for linear and circular DNA. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9393Non-histone chromosomal protein 6APRO_0000048565Add
BLAST

Proteomic databases

MaxQBiP11632.
PeptideAtlasiP11632.
TopDownProteomicsiP11632.

PTM databases

iPTMnetiP11632.

Interactioni

Subunit structurei

Weakly associates with the stable SPT16-POB3 heterodimer to form the FACT (yFACT or SNP) complex, which is associated with nucleosomes. Multiple molecules of NHP6 (NHP6A and/or NHP6B) are required to recruit the SPT16-POB3 heterodimer to DNA.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
STH1P325973EBI-12019,EBI-18410

GO - Molecular functioni

  • nucleosome binding Source: SGD

Protein-protein interaction databases

BioGridi36227. 136 interactions.
IntActiP11632. 61 interactions.
MINTiMINT-8285506.

Structurei

Secondary structure

1
93
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi17 – 193Combined sources
Helixi27 – 359Combined sources
Turni38 – 425Combined sources
Helixi48 – 514Combined sources
Turni52 – 543Combined sources
Helixi55 – 606Combined sources
Helixi63 – 7412Combined sources
Helixi77 – 804Combined sources
Helixi83 – 919Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CG7NMR-A1-93[»]
1J5NNMR-A1-93[»]
1LWMNMR-A1-93[»]
DisProtiDP00432.
ProteinModelPortaliP11632.
SMRiP11632. Positions 1-93.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11632.

Family & Domainsi

Sequence similaritiesi

Belongs to the NHP6 family.Curated
Contains 1 HMG box DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
InParanoidiP11632.
OMAiRTQVKED.
OrthoDBiEOG70KH25.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
InterProiIPR009071. HMG_box_dom.
[Graphical view]
PfamiPF00505. HMG_box. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P11632-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVTPREPKKR TTRKKKDPNA PKRALSAYMF FANENRDIVR SENPDITFGQ
60 70 80 90
VGKKLGEKWK ALTPEEKQPY EAKAQADKKR YESEKELYNA TLA
Length:93
Mass (Da):10,802
Last modified:October 1, 1989 - v1
Checksum:iA227296A12D440D8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15317 Genomic DNA. Translation: CAA33377.1.
M95912 Genomic RNA. Translation: AAA34754.1.
Z49219 Genomic DNA. Translation: CAA89171.1.
Z71255 Genomic DNA. Translation: CAA94998.1.
AY693230 Genomic DNA. Translation: AAT93249.1.
BK006949 Genomic DNA. Translation: DAA11475.1.
PIRiA35072.
RefSeqiNP_015377.1. NM_001184149.1.

Genome annotation databases

EnsemblFungiiYPR052C; YPR052C; YPR052C.
GeneIDi856165.
KEGGisce:YPR052C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15317 Genomic DNA. Translation: CAA33377.1.
M95912 Genomic RNA. Translation: AAA34754.1.
Z49219 Genomic DNA. Translation: CAA89171.1.
Z71255 Genomic DNA. Translation: CAA94998.1.
AY693230 Genomic DNA. Translation: AAT93249.1.
BK006949 Genomic DNA. Translation: DAA11475.1.
PIRiA35072.
RefSeqiNP_015377.1. NM_001184149.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CG7NMR-A1-93[»]
1J5NNMR-A1-93[»]
1LWMNMR-A1-93[»]
DisProtiDP00432.
ProteinModelPortaliP11632.
SMRiP11632. Positions 1-93.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36227. 136 interactions.
IntActiP11632. 61 interactions.
MINTiMINT-8285506.

PTM databases

iPTMnetiP11632.

Proteomic databases

MaxQBiP11632.
PeptideAtlasiP11632.
TopDownProteomicsiP11632.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPR052C; YPR052C; YPR052C.
GeneIDi856165.
KEGGisce:YPR052C.

Organism-specific databases

EuPathDBiFungiDB:YPR052C.
SGDiS000006256. NHP6A.

Phylogenomic databases

GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
InParanoidiP11632.
OMAiRTQVKED.
OrthoDBiEOG70KH25.

Enzyme and pathway databases

BioCyciYEAST:G3O-34205-MONOMER.
ReactomeiR-SCE-211227. Activation of DNA fragmentation factor.

Miscellaneous databases

EvolutionaryTraceiP11632.
PROiP11632.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
InterProiIPR009071. HMG_box_dom.
[Graphical view]
PfamiPF00505. HMG_box. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Duplicated NHP6 genes of Saccharomyces cerevisiae encode proteins homologous to bovine high mobility group protein 1."
    Kolodrubetz D., Burgum A.
    J. Biol. Chem. 265:3234-3239(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: DBY1091 / DKY1.
  2. "Localized mutagenesis and evidence for post-transcriptional regulation of MAK3. A putative N-acetyltransferase required for double-stranded RNA virus propagation in Saccharomyces cerevisiae."
    Tercero J.C., Riles L.E., Wickner R.B.
    J. Biol. Chem. 267:20270-20276(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. "DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B. Consequences for nucleoprotein complex assembly and chromatin condensation."
    Paull T.T., Johnson R.C.
    J. Biol. Chem. 270:8744-8754(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro."
    Paull T.T., Carey M., Johnson R.C.
    Genes Dev. 10:2769-2781(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Determinants of DNA binding and bending by the Saccharomyces cerevisiae high mobility group protein NHP6A that are important for its biological activities. Role of the unique N terminus and putative intercalating methionine."
    Yen Y.-M., Wong B., Johnson R.C.
    J. Biol. Chem. 273:4424-4435(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: DNA-BINDING, MUTAGENESIS OF PRO-18; PRO-21; TYR-28; MET-29; PHE-30 AND PHE-31.
  9. "Chromatin-mediated transcriptional regulation by the yeast architectural factors NHP6A and NHP6B."
    Moreira J.M.A., Holmberg S.
    EMBO J. 19:6804-6813(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "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] [Europe PMC] [Abstract]
    Cited for: ASSOCIATION WITH THE SPT16-POB3 DIMER AND NUCLEOSOMES, FUNCTION OF THE FACT COMPLEX.
  11. "Nhp6, an HMG1 protein, functions in SNR6 transcription by RNA polymerase III in S. cerevisiae."
    Kruppa M., Moir R.D., Kolodrubetz D., Willis I.M.
    Mol. Cell 7:309-318(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. Erratum
    Kruppa M., Moir R.D., Kolodrubetz D., Willis I.M.
    Mol. Cell 8:727-727(2001)
  13. "High-mobility-group proteins NHP6A and NHP6B participate in activation of the RNA polymerase III SNR6 gene."
    Lopez S., Livingstone-Zatchej M., Jourdain S., Thoma F., Sentenac A., Marsolier M.-C.
    Mol. Cell. Biol. 21:3096-3104(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  14. "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] [Europe PMC] [Abstract]
    Cited for: ASSOCIATION WITH THE SPT16-POB3 DIMER.
  15. "Nuclear localization of the Saccharomyces cerevisiae HMG protein NHP6A occurs by a Ran-independent nonclassical pathway."
    Yen Y.-M., Roberts P.M., Johnson R.C.
    Traffic 2:449-464(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  16. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  17. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE FACT COMPLEX.
  18. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  19. "Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes."
    Skoko D., Wong B., Johnson R.C., Marko J.F.
    Biochemistry 43:13867-13874(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: DNA-BINDING.
  20. "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] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  21. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE FACT COMPLEX.
  22. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE FACT COMPLEX.
  23. "Nhp6 is a transcriptional initiation fidelity factor for RNA polymerase III transcription in vitro and in vivo."
    Kassavetis G.A., Steiner D.F.
    J. Biol. Chem. 281:7445-7451(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  24. "Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding."
    Allain F.H.-T., Yen Y.-M., Masse J.E., Schultze P., Dieckmann T., Johnson R.C., Feigon J.
    EMBO J. 18:2563-2579(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR IN COMPLEX WITH DNA.
  25. "The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding."
    Masse J.E., Wong B., Yen Y.-M., Allain F.H.-T., Johnson R.C., Feigon J.
    J. Mol. Biol. 323:263-284(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR IN COMPLEX WITH DNA.

Entry informationi

Entry nameiNHP6A_YEAST
AccessioniPrimary (citable) accession number: P11632
Secondary accession number(s): D6W459
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: June 8, 2016
This is version 157 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 3870 molecules/cell in log phase SD medium.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 XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: 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.