Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

H/ACA ribonucleoprotein complex non-core subunit NAF1

Gene

NAF1

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

RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex and disappears during maturation of the complex and is replaced by GAR1 to yield mature H/ACA snoRNPs complex. Acts as a competitive binder for CBF5 probably required to prevent non-cognate RNAs from being loaded during transport of the particle by inducing a non-productive conformation of CBF5.5 Publications

GO - Molecular functioni

  • RNA binding Source: SGD

GO - Biological processi

  • box H/ACA snoRNP assembly Source: SGD
  • pseudouridine synthesis Source: InterPro
  • rRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33145-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
H/ACA ribonucleoprotein complex non-core subunit NAF1
Alternative name(s):
Nuclear assembly factor 1
Gene namesi
Name:NAF1
Ordered Locus Names:YNL124W
ORF Names:N1888
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL124W.
SGDiS000005068. NAF1.

Subcellular locationi

GO - Cellular componenti

  • intracellular ribonucleoprotein complex Source: UniProtKB-KW
  • nucleoplasm Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 492492H/ACA ribonucleoprotein complex non-core subunit NAF1PRO_0000203428Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei255 – 2551PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53919.

PTM databases

iPTMnetiP53919.

Interactioni

Subunit structurei

During assembly of the complex, component of the small nucleolar ribonucleoprotein particles containing H/ACA-type snoRNAs (H/ACA snoRNPs) which contains CBF5, NAF1, NHP2 and NOP10 proteins. Interacts with SHQ1. Interacts directly with CBF5. Interacts with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (RPB1).4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CBF5P333226EBI-28887,EBI-4105
NHP2P324953EBI-28887,EBI-12014

Protein-protein interaction databases

BioGridi35703. 96 interactions.
DIPiDIP-4345N.
IntActiP53919. 255 interactions.
MINTiMINT-501196.

Structurei

Secondary structure

1
492
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi137 – 14711Combined sources
Beta strandi150 – 1556Combined sources
Beta strandi169 – 1724Combined sources
Beta strandi177 – 1804Combined sources
Beta strandi183 – 1864Combined sources
Beta strandi188 – 1903Combined sources
Beta strandi192 – 1965Combined sources
Helixi199 – 2013Combined sources
Helixi202 – 2098Combined sources
Turni210 – 2134Combined sources
Beta strandi214 – 2196Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2V3MX-ray2.74A/B/C/D/E/F109-232[»]
ProteinModelPortaliP53919.
SMRiP53919. Positions 120-220.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP53919.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni172 – 23059RNA-bindingAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi55 – 8127Ser-richAdd
BLAST
Compositional biasi361 – 45696Pro-richAdd
BLAST
Compositional biasi419 – 48870Gln-richAdd
BLAST

Domaini

The central region (136-221) reveals a striking structural homology with the core domain of GAR1.1 Publication

Sequence similaritiesi

Belongs to the NAF1 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000004697.
InParanoidiP53919.
KOiK14763.
OMAiINTEDCD.
OrthoDBiEOG7JDR6J.

Family and domain databases

InterProiIPR007504. H/ACA_rnp_Gar1/Naf1.
IPR009000. Transl_B-barrel.
[Graphical view]
PfamiPF04410. Gar1. 1 hit.
[Graphical view]
SUPFAMiSSF50447. SSF50447. 1 hit.

Sequencei

Sequence statusi: Complete.

P53919-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDDLFSKAL ENPDQDLNVE LPKDDVDLGL LGDGGNERKT DEPVADAERS
60 70 80 90 100
TGLGSGSSES ESDSGSDSDS DSGSSGSEDD SADQDVEGED EGGDAIENED
110 120 130 140 150
EDEDPSPSGP ILSKNEILEE TVPELPEDYE ISEKTIITPI GVLKSAFENN
160 170 180 190 200
IIIHATMSGE KRVLKEGSIF CLEDRTLIGM LTEVFGPLQN PFYRIKLPDS
210 220 230 240 250
KKNLFDELKV RLGEKAFIVT PDAHWIDTFE LKRNKGTDAS NGYDEELPEE
260 270 280 290 300
EQEFSDDEKE ALFKKMKKQQ RQRKKRDNRK LANDSDNVKV KRARQPKANS
310 320 330 340 350
LPKLVPPLGM SSNAPMQHGY KSRNARENIK RESSATSNRN GSSPVPITQH
360 370 380 390 400
HQQQFSANNY PFPQQPNGMP YPPYSPFPQP TNFQYPPPPF GQATPAQFSN
410 420 430 440 450
TVPYGSLPPA YNNMSPPTQQ SFMPMTQSQP PLPYGVPPMN QMQNPMYIQP
460 470 480 490
PPQAPPQGNG NFQQVMELHQ ILLQQQQQQH QYQHQHQQDP RT
Length:492
Mass (Da):54,949
Last modified:October 1, 1996 - v1
Checksum:i5A496278070F6255
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti378 – 3781P → A in strain: YJM269, YJM270, YJM326 and YJM1129. 1 Publication
Natural varianti423 – 4231M → I in strain: YJM627. 1 Publication
Natural varianti424 – 4241P → S in strain: YJM269, YJM270, YJM326 and YJM1129. 1 Publication
Natural varianti426 – 4261T → A in strain: SK1, V1-09, YJM269, YJM270, YJM280, YJM320, YJM326, YJM339, YJM627, YJM789 and YJM1129. 1 Publication
Natural varianti480 – 4801H → N in strain: V1-09 and YJM627. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z69382 Genomic DNA. Translation: CAA93381.1.
Z71400 Genomic DNA. Translation: CAA96005.1.
EF125216 Genomic DNA. Translation: ABN58535.1.
EF125217 Genomic DNA. Translation: ABN58543.1.
EF125218 Genomic DNA. Translation: ABN58552.1.
EF125219 Genomic DNA. Translation: ABN58561.1.
EF125220 Genomic DNA. Translation: ABN58570.1.
EF125221 Genomic DNA. Translation: ABN58579.1.
EF125222 Genomic DNA. Translation: ABN58588.1.
EF125223 Genomic DNA. Translation: ABN58597.1.
EF125224 Genomic DNA. Translation: ABN58606.1.
EF125225 Genomic DNA. Translation: ABN58615.1.
EF125226 Genomic DNA. Translation: ABN58624.1.
EF125228 Genomic DNA. Translation: ABN58642.1.
BK006947 Genomic DNA. Translation: DAA10425.1.
PIRiS63065.
RefSeqiNP_014275.3. NM_001182962.3.

Genome annotation databases

EnsemblFungiiYNL124W; YNL124W; YNL124W.
GeneIDi855599.
KEGGisce:YNL124W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z69382 Genomic DNA. Translation: CAA93381.1.
Z71400 Genomic DNA. Translation: CAA96005.1.
EF125216 Genomic DNA. Translation: ABN58535.1.
EF125217 Genomic DNA. Translation: ABN58543.1.
EF125218 Genomic DNA. Translation: ABN58552.1.
EF125219 Genomic DNA. Translation: ABN58561.1.
EF125220 Genomic DNA. Translation: ABN58570.1.
EF125221 Genomic DNA. Translation: ABN58579.1.
EF125222 Genomic DNA. Translation: ABN58588.1.
EF125223 Genomic DNA. Translation: ABN58597.1.
EF125224 Genomic DNA. Translation: ABN58606.1.
EF125225 Genomic DNA. Translation: ABN58615.1.
EF125226 Genomic DNA. Translation: ABN58624.1.
EF125228 Genomic DNA. Translation: ABN58642.1.
BK006947 Genomic DNA. Translation: DAA10425.1.
PIRiS63065.
RefSeqiNP_014275.3. NM_001182962.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2V3MX-ray2.74A/B/C/D/E/F109-232[»]
ProteinModelPortaliP53919.
SMRiP53919. Positions 120-220.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35703. 96 interactions.
DIPiDIP-4345N.
IntActiP53919. 255 interactions.
MINTiMINT-501196.

PTM databases

iPTMnetiP53919.

Proteomic databases

MaxQBiP53919.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL124W; YNL124W; YNL124W.
GeneIDi855599.
KEGGisce:YNL124W.

Organism-specific databases

EuPathDBiFungiDB:YNL124W.
SGDiS000005068. NAF1.

Phylogenomic databases

GeneTreeiENSGT00390000004697.
InParanoidiP53919.
KOiK14763.
OMAiINTEDCD.
OrthoDBiEOG7JDR6J.

Enzyme and pathway databases

BioCyciYEAST:G3O-33145-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP53919.
PROiP53919.

Family and domain databases

InterProiIPR007504. H/ACA_rnp_Gar1/Naf1.
IPR009000. Transl_B-barrel.
[Graphical view]
PfamiPF04410. Gar1. 1 hit.
[Graphical view]
SUPFAMiSSF50447. SSF50447. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The DNA sequence of cosmid 14-13b from chromosome XIV of Saccharomyces cerevisiae reveals an unusually high number of overlapping open reading frames."
    de Antoni A., D'Angelo M., Dal Pero F., Sartorello F., Pandolfo D., Pallavicini A., Lanfranchi G., Valle G.
    Yeast 13:261-266(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "A 43.5 kb segment of yeast chromosome XIV, which contains MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1, predicts an adenosine deaminase gene and 14 new open reading frames."
    Mallet L., Bussereau F., Jacquet M.
    Yeast 11:1195-1209(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-50.
    Strain: ATCC 204508 / S288c.
  5. "Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast."
    Sinha H., David L., Pascon R.C., Clauder-Muenster S., Krishnakumar S., Nguyen M., Shi G., Dean J., Davis R.W., Oefner P.J., McCusker J.H., Steinmetz L.M.
    Genetics 180:1661-1670(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 371-492, VARIANTS ALA-378; ILE-423; SER-424; ALA-426 AND ASN-480.
    Strain: ATCC 200060 / W303, S103, SK1, V1-09, YJM 1129, YJM 269, YJM 270, YJM 320, YJM 326, YJM 339, YJM 627 and YJM230.
  6. "The Shq1p.Naf1p complex is required for box H/ACA small nucleolar ribonucleoprotein particle biogenesis."
    Yang P.K., Rotondo G., Porras T., Legrain P., Chanfreau G.
    J. Biol. Chem. 277:45235-45242(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH CBF5; SHQ1 AND NHP2.
  7. "Naf1p, an essential nucleoplasmic factor specifically required for accumulation of box H/ACA small nucleolar RNPs."
    Dez C., Noaillac-Depeyre J., Caizergues-Ferrer M., Henry Y.
    Mol. Cell. Biol. 22:7053-7065(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  8. "Naf1 p is a box H/ACA snoRNP assembly factor."
    Fatica A., Dlakic M., Tollervey D.
    RNA 8:1502-1514(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RNA-BINDING, SUBCELLULAR LOCATION, INTERACTION WITH CBF5; NHP2 AND RPB1.
  9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of the RNA binding protein Naf1p during H/ACA snoRNP assembly."
    Yang P.K., Hoareau C., Froment C., Monsarrat B., Henry Y., Chanfreau G.
    Mol. Cell. Biol. 25:3295-3304(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CBF5.
  12. "The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae."
    Ballarino M., Morlando M., Pagano F., Fatica A., Bozzoni I.
    Mol. Cell. Biol. 25:5396-5403(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CBF5 AND NHP2.
  13. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-255, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  14. "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] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-255, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-255, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p."
    Leulliot N., Godin K.S., Hoareau-Aveilla C., Quevillon-Cheruel S., Varani G., Henry Y., Van Tilbeurgh H.
    J. Mol. Biol. 371:1338-1353(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.74 ANGSTROMS) OF 109-234, DOMAIN.

Entry informationi

Entry nameiNAF1_YEAST
AccessioniPrimary (citable) accession number: P53919
Secondary accession number(s): B0KZR2
, B0KZS1, B0KZT9, B0KZZ3, B0L002, D6W159
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 6, 2016
This is version 127 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 1810 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: 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.