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Protein

Nuclear polyadenylated RNA-binding protein 3

Gene

NAB3

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

May be required for packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Binds to poly(A)+ RNA. Appears to act in the maintenance of CLN3 mRNA levels.1 Publication

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • 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-34083-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear polyadenylated RNA-binding protein 3
Gene namesi
Name:NAB3
Synonyms:HMD1
Ordered Locus Names:YPL190C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL190C.
SGDiS000006111. NAB3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • Nrd1 complex Source: SGD
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 802802Nuclear polyadenylated RNA-binding protein 3PRO_0000081657Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei86 – 861PhosphothreonineCombined sources
Modified residuei451 – 4511PhosphothreonineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP38996.

PTM databases

iPTMnetiP38996.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
NRD1P536173EBI-11776,EBI-12228

Protein-protein interaction databases

BioGridi35993. 122 interactions.
DIPiDIP-3980N.
IntActiP38996. 22 interactions.
MINTiMINT-536351.

Structurei

Secondary structure

1
802
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi331 – 3366Combined sources
Beta strandi339 – 3413Combined sources
Helixi344 – 3518Combined sources
Helixi352 – 3543Combined sources
Beta strandi357 – 3626Combined sources
Beta strandi364 – 37310Combined sources
Helixi374 – 38411Combined sources
Beta strandi387 – 3893Combined sources
Turni391 – 3933Combined sources
Beta strandi395 – 3984Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2KVINMR-A321-415[»]
2L41NMR-A328-404[»]
2XNQX-ray1.30A329-404[»]
2XNRX-ray1.60A329-404[»]
ProteinModelPortaliP38996.
SMRiP38996. Positions 329-402.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38996.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini330 – 40172RRMPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi68 – 714Poly-Glu
Compositional biasi87 – 937Poly-Glu
Compositional biasi101 – 1066Poly-Asp
Compositional biasi108 – 1158Poly-Glu
Compositional biasi116 – 12712Poly-AspAdd
BLAST
Compositional biasi128 – 13710Poly-Glu
Compositional biasi603 – 6086Poly-Gln
Compositional biasi644 – 6485Poly-Pro
Compositional biasi698 – 7036Poly-Gln
Compositional biasi723 – 7286Poly-Gln
Compositional biasi765 – 7684Poly-Pro
Compositional biasi769 – 78416Poly-GlnAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000113718.
InParanoidiP38996.
KOiK15561.
OMAiNKITEMH.
OrthoDBiEOG092C3H1L.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
3.40.50.800. 1 hit.
InterProiIPR004154. Anticodon-bd.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF52954. SSF52954. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38996-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDENHNSDV QDIPSPELSV DSNSNENELM NNSSADDGIE FDAPEEEREA
60 70 80 90 100
EREEENEEQH ELEDVNDEEE EDKEEKGEEN GEVINTEEEE EEEHQQKGGN
110 120 130 140 150
DDDDDDNEEE EEEEEDDDDD DDDDDDDEEE EEEEEEEGND NSSVGSDSAA
160 170 180 190 200
EDGEDEEDKK DKTKDKEVEL RRETLEKEQK DVDEAIKKIT REENDNTHFP
210 220 230 240 250
TNMENVNYDL LQKQVKYIMD SNMLNLPQFQ HLPQEEKMSA ILAMLNSNSD
260 270 280 290 300
TALSVPPHDS TISTTASASA TSGARSNDQR KPPLSDAQRR MRFPRADLSK
310 320 330 340 350
PITEEEHDRY AAYLHGENKI TEMHNIPPKS RLFIGNLPLK NVSKEDLFRI
360 370 380 390 400
FSPYGHIMQI NIKNAFGFIQ FDNPQSVRDA IECESQEMNF GKKLILEVSS
410 420 430 440 450
SNARPQFDHG DHGTNSSSTF ISSAKRPFQT ESGDMYNDDN GAGYKKSRRH
460 470 480 490 500
TVSCNIFVKR TADRTYAIEV FNRFRDGTGL ETDMIFLKPR MELGKLINDA
510 520 530 540 550
AYNGVWGVVL VNKTHNVDVQ TFYKGSQGET KFDEYISISA DDAVAIFNNI
560 570 580 590 600
KNNRNNSRPT DYRAMSHQQN IYGAPPLPVP NGPAVGPPPQ TNYYQGYSMP
610 620 630 640 650
PPQQQQQQPY GNYGMPPPSH DQGYGSQPPI PMNQSYGRYQ TSIPPPPPQQ
660 670 680 690 700
QIPQGYGRYQ AGPPPQPPSQ TPMDQQQLLS AIQNLPPNVV SNLLSMAQQQ
710 720 730 740 750
QQQPHAQQQL VGLIQSMQGQ APQQQQQQLG GYSSMNSSSP PPMSTNYNGQ
760 770 780 790 800
NISAKPSAPP MSHQPPPPQQ QQQQQQQQQQ QQQQPAGNNV QSLLDSLAKL

QK
Length:802
Mass (Da):90,439
Last modified:February 1, 1995 - v1
Checksum:iCD6D2C7F24A44993
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti341 – 3411N → I in BAA07154 (PubMed:7476874).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U05314 Genomic DNA. Translation: AAA81910.1.
D37935 Genomic DNA. Translation: BAA07154.1.
Z73546 Genomic DNA. Translation: CAA97903.1.
BK006949 Genomic DNA. Translation: DAA11244.1.
PIRiS48529.
RefSeqiNP_015134.1. NM_001184004.1.

Genome annotation databases

EnsemblFungiiYPL190C; YPL190C; YPL190C.
GeneIDi855911.
KEGGisce:YPL190C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U05314 Genomic DNA. Translation: AAA81910.1.
D37935 Genomic DNA. Translation: BAA07154.1.
Z73546 Genomic DNA. Translation: CAA97903.1.
BK006949 Genomic DNA. Translation: DAA11244.1.
PIRiS48529.
RefSeqiNP_015134.1. NM_001184004.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2KVINMR-A321-415[»]
2L41NMR-A328-404[»]
2XNQX-ray1.30A329-404[»]
2XNRX-ray1.60A329-404[»]
ProteinModelPortaliP38996.
SMRiP38996. Positions 329-402.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35993. 122 interactions.
DIPiDIP-3980N.
IntActiP38996. 22 interactions.
MINTiMINT-536351.

PTM databases

iPTMnetiP38996.

Proteomic databases

MaxQBiP38996.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL190C; YPL190C; YPL190C.
GeneIDi855911.
KEGGisce:YPL190C.

Organism-specific databases

EuPathDBiFungiDB:YPL190C.
SGDiS000006111. NAB3.

Phylogenomic databases

HOGENOMiHOG000113718.
InParanoidiP38996.
KOiK15561.
OMAiNKITEMH.
OrthoDBiEOG092C3H1L.

Enzyme and pathway databases

BioCyciYEAST:G3O-34083-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP38996.
PROiP38996.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
3.40.50.800. 1 hit.
InterProiIPR004154. Anticodon-bd.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF52954. SSF52954. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNAB3_YEAST
AccessioniPrimary (citable) accession number: P38996
Secondary accession number(s): D6W3H8, Q07034
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 7, 2016
This is version 147 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 5830 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.