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Protein

Protein NRD1

Gene

NRD1

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

Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • protein domain specific binding Source: SGD
  • RNA binding Source: SGD
  • transcription regulatory region RNA binding Source: SGD

GO - Biological processi

  • antisense RNA transcript catabolic process Source: SGD
  • CUT catabolic process Source: SGD
  • mRNA 3'-end processing Source: SGD
  • nuclear mRNA surveillance Source: SGD
  • snoRNA 3'-end processing Source: SGD
  • snRNA 3'-end processing Source: SGD
  • termination of RNA polymerase II transcription, exosome-dependent Source: SGD
  • tRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33248-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein NRD1
Gene namesi
Name:NRD1
Ordered Locus Names:YNL251C
ORF Names:N0868
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL251C.
SGDiS000005195. NRD1.

Subcellular locationi

GO - Cellular componenti

  • Nrd1 complex Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 575575Protein NRD1PRO_0000081688Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei263 – 2631PhosphoserineCombined sources
Modified residuei265 – 2651PhosphoserineCombined sources
Modified residuei271 – 2711PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53617.
PeptideAtlasiP53617.

PTM databases

iPTMnetiP53617.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
NAB3P389963EBI-12228,EBI-11776

GO - Molecular functioni

  • protein domain specific binding Source: SGD

Protein-protein interaction databases

BioGridi35588. 284 interactions.
DIPiDIP-6778N.
IntActiP53617. 23 interactions.
MINTiMINT-615670.

Structurei

Secondary structure

1
575
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 53Combined sources
Helixi7 – 159Combined sources
Helixi16 – 194Combined sources
Beta strandi21 – 233Combined sources
Helixi26 – 3813Combined sources
Helixi39 – 424Combined sources
Helixi43 – 5614Combined sources
Helixi59 – 613Combined sources
Helixi62 – 8120Combined sources
Helixi94 – 11522Combined sources
Helixi118 – 13417Combined sources
Turni135 – 1395Combined sources
Turni143 – 1464Combined sources
Helixi148 – 1514Combined sources
Beta strandi331 – 3333Combined sources
Beta strandi340 – 3456Combined sources
Beta strandi347 – 3504Combined sources
Helixi352 – 3554Combined sources
Beta strandi356 – 3605Combined sources
Beta strandi365 – 3717Combined sources
Turni372 – 3754Combined sources
Beta strandi376 – 3827Combined sources
Helixi384 – 39613Combined sources
Beta strandi397 – 3993Combined sources
Beta strandi401 – 4077Combined sources
Helixi418 – 4203Combined sources
Helixi426 – 4283Combined sources
Helixi429 – 4379Combined sources
Beta strandi440 – 4434Combined sources
Beta strandi445 – 4495Combined sources
Helixi450 – 4534Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LO6NMR-A1-153[»]
2M88NMR-A307-491[»]
2MOWNMR-A1-153[»]
3CLJX-ray2.10A6-151[»]
ProteinModelPortaliP53617.
SMRiP53617. Positions 1-154, 307-491.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP53617.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 153153CIDPROSITE-ProRule annotationAdd
BLAST
Domaini339 – 40971RRMPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi541 – 5444Poly-Ala
Compositional biasi567 – 5748Poly-Gln

Sequence similaritiesi

Contains 1 CID domain.PROSITE-ProRule annotation
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000248757.
InParanoidiP53617.
KOiK15560.
OMAiCCDYQHG.
OrthoDBiEOG7X9GGZ.

Family and domain databases

Gene3Di1.25.40.90. 1 hit.
3.30.70.330. 1 hit.
InterProiIPR006569. CID_dom.
IPR008942. ENTH_VHS.
IPR012677. Nucleotide-bd_a/b_plait.
IPR006903. RNA_pol_II-bd.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF04818. CTD_bind. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00582. RPR. 1 hit.
SM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF48464. SSF48464. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS51391. CID. 1 hit.
PS50102. RRM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P53617-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQQDDDFQNF VATLESFKDL KSGISGSRIK KLTTYALDHI DIESKIISLI
60 70 80 90 100
IDYSRLCPDS HKLGSLYIID SIGRAYLDET RSNSNSSSNK PGTCAHAINT
110 120 130 140 150
LGEVIQELLS DAIAKSNQDH KEKIRMLLDI WDRSGLFQKS YLNAIRSKCF
160 170 180 190 200
AMDISNNTAN TASQQLSLDP KQRSKQILSN LKKSPPLNLN ISLPTDLTST
210 220 230 240 250
DPAKQQAALF QVIAALQKHF KTLPSHTSVG TVAPPQAHTI TEYGSRRERE
260 270 280 290 300
RERERYNSRR NRSRSPPAPF SQPSTGRKDR YPSVAQDQYS IGAPNTTFGT
310 320 330 340 350
NNHHLYPDEL NVSNNPHYRP KPVSYDSTLP PDHIKVYSRT LFIGGVPLNM
360 370 380 390 400
KEWDLANVLK PFAEVQSVIL NNSRKHAFVK VYSRHEAENV LQNFNKDGAL
410 420 430 440 450
PLRTRWGVGF GPRDCCDYQH GYSIIPMHRL TDADKKWSVS AQWGGTSGQP
460 470 480 490 500
LVTGIVFEEP DIIVGEGVSS KAISQKMPTD SGRNGPRSGK PNKSGSISSI
510 520 530 540 550
SPVPYGNAPL ASPPPQQYVQ PMMQQPYGYA PNQPLPSQGP AAAAPPVPQQ
560 570
QFDPTAQLNS LMNMLNQQQQ QQQQS
Length:575
Mass (Da):63,859
Last modified:October 1, 1996 - v1
Checksum:i75082BDB0C42AE37
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28487 Genomic DNA. Translation: AAC49568.1.
X96722 Genomic DNA. Translation: CAA65493.1.
Z71527 Genomic DNA. Translation: CAA96158.1.
BK006947 Genomic DNA. Translation: DAA10308.1.
PIRiS59740.
RefSeqiNP_014148.1. NM_001183089.1.

Genome annotation databases

EnsemblFungiiYNL251C; YNL251C; YNL251C.
GeneIDi855470.
KEGGisce:YNL251C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28487 Genomic DNA. Translation: AAC49568.1.
X96722 Genomic DNA. Translation: CAA65493.1.
Z71527 Genomic DNA. Translation: CAA96158.1.
BK006947 Genomic DNA. Translation: DAA10308.1.
PIRiS59740.
RefSeqiNP_014148.1. NM_001183089.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LO6NMR-A1-153[»]
2M88NMR-A307-491[»]
2MOWNMR-A1-153[»]
3CLJX-ray2.10A6-151[»]
ProteinModelPortaliP53617.
SMRiP53617. Positions 1-154, 307-491.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35588. 284 interactions.
DIPiDIP-6778N.
IntActiP53617. 23 interactions.
MINTiMINT-615670.

PTM databases

iPTMnetiP53617.

Proteomic databases

MaxQBiP53617.
PeptideAtlasiP53617.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL251C; YNL251C; YNL251C.
GeneIDi855470.
KEGGisce:YNL251C.

Organism-specific databases

EuPathDBiFungiDB:YNL251C.
SGDiS000005195. NRD1.

Phylogenomic databases

HOGENOMiHOG000248757.
InParanoidiP53617.
KOiK15560.
OMAiCCDYQHG.
OrthoDBiEOG7X9GGZ.

Enzyme and pathway databases

BioCyciYEAST:G3O-33248-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP53617.
NextBioi979415.
PROiP53617.

Family and domain databases

Gene3Di1.25.40.90. 1 hit.
3.30.70.330. 1 hit.
InterProiIPR006569. CID_dom.
IPR008942. ENTH_VHS.
IPR012677. Nucleotide-bd_a/b_plait.
IPR006903. RNA_pol_II-bd.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF04818. CTD_bind. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00582. RPR. 1 hit.
SM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF48464. SSF48464. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS51391. CID. 1 hit.
PS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1."
    Steinmetz E.J., Brow D.A.
    Mol. Cell. Biol. 16:6993-7003(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequence analysis of the 33 kb long region between ORC5 and SUI1 from the left arm of chromosome XIV from Saccharomyces cerevisiae."
    Sen-Gupta M., Gueldener U., Beinhauer J.D., Fiedler T.A., Hegemann J.H.
    Yeast 13:849-860(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. "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.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "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-263 AND SER-265, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  7. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "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-263; SER-265 AND SER-271, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNRD1_YEAST
AccessioniPrimary (citable) accession number: P53617
Secondary accession number(s): D6W0U2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: May 11, 2016
This is version 139 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 19600 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.