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Protein

Partner of Y14 and mago

Gene

PYM1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Key regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation. Acts as an EJC disassembly factor, allowing translation-dependent EJC removal and recycling by disrupting mature EJC from spliced mRNAs. Its association with the 40S ribosomal subunit probably prevents a translation-independent disassembly of the EJC from spliced mRNAs, by restricting its activity to mRNAs that have been translated. Interferes with NMD and enhances translation of spliced mRNAs, probably by antagonizing EJC functions. May bind RNA; the relevance of RNA-binding remains unclear in vivo, RNA-binding was detected by PubMed:14968132, while PubMed:19410547 did not detect RNA-binding activity independently of the EJC.2 Publications

GO - Molecular functioni

  • ribosome binding Source: UniProtKB
  • RNA binding Source: UniProtKB

GO - Biological processi

  • exon-exon junction complex disassembly Source: HGNC
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
  • positive regulation of translation Source: UniProtKB

Keywordsi

Molecular functionRNA-binding
Biological processNonsense-mediated mRNA decay, Translation regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Partner of Y14 and magoBy similarity
Alternative name(s):
PYM homolog 1 exon junction complex-associated factorImported
Protein wibg homolog
Gene namesi
Name:PYM1Imported
Synonyms:PYM, WIBG
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:30258. PYM1.

Subcellular locationi

GO - Cellular componenti

  • cell junction Source: HPA
  • cytosol Source: HPA
  • exon-exon junction complex Source: UniProtKB
  • nucleolus Source: HPA
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: HPA

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi84305.
OpenTargetsiENSG00000170473.
PharmGKBiPA142670574.

Polymorphism and mutation databases

BioMutaiWIBG.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002872851 – 204Partner of Y14 and magoAdd BLAST204

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei6PhosphoserineCombined sources1
Modified residuei64PhosphoserineCombined sources1
Modified residuei72PhosphothreonineCombined sources1
Modified residuei117PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9BRP8.
MaxQBiQ9BRP8.
PaxDbiQ9BRP8.
PeptideAtlasiQ9BRP8.
PRIDEiQ9BRP8.

PTM databases

iPTMnetiQ9BRP8.
PhosphoSitePlusiQ9BRP8.

Expressioni

Gene expression databases

BgeeiENSG00000170473.
CleanExiHS_WIBG.
ExpressionAtlasiQ9BRP8. baseline and differential.
GenevisibleiQ9BRP8. HS.

Organism-specific databases

HPAiCAB012803.
HPA039717.
HPA046200.

Interactioni

Subunit structurei

Interacts (via N-terminus) with MAGOH and RBM8A; the interaction is direct. Associates (eIF2A-like region) with the 40S ribosomal subunit and the 48S preinitiation complex.3 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi124031. 76 interactors.
DIPiDIP-48413N.
IntActiQ9BRP8. 30 interactors.
MINTiMINT-3060675.
STRINGi9606.ENSP00000386156.

Structurei

3D structure databases

ProteinModelPortaliQ9BRP8.
SMRiQ9BRP8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 33Required for interaction with MAGOH and RBM8AAdd BLAST33
Regioni152 – 204eIF2A-likeAdd BLAST53

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili82 – 116Sequence analysisAdd BLAST35
Coiled coili145 – 204Sequence analysisAdd BLAST60

Domaini

The eIF2A-like region shares sequence similarity with eIF2A and mediates the interaction with the 40S ribosomal subunit and the 48S preinitiation complex.1 Publication

Sequence similaritiesi

Belongs to the pym family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG4325. Eukaryota.
ENOG4111KHQ. LUCA.
GeneTreeiENSGT00730000111107.
HOGENOMiHOG000215176.
HOVERGENiHBG097451.
InParanoidiQ9BRP8.
KOiK14294.
OMAiKSAKRNM.
OrthoDBiEOG091G0XQ3.
PhylomeDBiQ9BRP8.
TreeFamiTF324615.

Family and domain databases

InterProiView protein in InterPro
IPR015362. WIBG_fam.
PfamiView protein in Pfam
PF09282. Mago-bind. 1 hit.
SMARTiView protein in SMART
SM01273. Mago-bind. 1 hit.
SUPFAMiSSF101931. SSF101931. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BRP8-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEAAGSPAAT ETGKYIASTQ RPDGTWRKQR RVKEGYVPQE EVPVYENKYV
60 70 80 90 100
KFFKSKPELP PGLSPEATAP VTPSRPEGGE PGLSKTAKRN LKRKEKRRQQ
110 120 130 140 150
QEKGEAEALS RTLDKVSLEE TAQLPSAPQG SRAAPTAASD QPDSAATTEK
160 170 180 190 200
AKKIKNLKKK LRQVEELQQR IQAGEVSQPS KEQLEKLARR RALEEELEDL

ELGL
Length:204
Mass (Da):22,656
Last modified:June 1, 2001 - v1
Checksum:i087B901279007C05
GO
Isoform 2 (identifier: Q9BRP8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-12: MEAAGSPAATET → MATPYVTDETG

Show »
Length:203
Mass (Da):22,705
Checksum:i67BA3B0E86D8C581
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti147T → S in CAD30677 (PubMed:12438415).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03229766E → Q. Corresponds to variant dbSNP:rs3802998Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0254301 – 12MEAAG…AATET → MATPYVTDETG in isoform 2. 1 PublicationAdd BLAST12

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ459406 mRNA. Translation: CAD30677.1.
AK096922 mRNA. Translation: BAC04897.1.
AC023055 Genomic DNA. No translation available.
AC025162 Genomic DNA. No translation available.
BC006135 mRNA. Translation: AAH06135.1.
BC014976 mRNA. Translation: AAH14976.1.
CCDSiCCDS41795.1. [Q9BRP8-1]
CCDS44916.1. [Q9BRP8-2]
RefSeqiNP_001137325.1. NM_001143853.1. [Q9BRP8-2]
NP_115721.1. NM_032345.2. [Q9BRP8-1]
UniGeneiHs.505687.
Hs.524488.

Genome annotation databases

EnsembliENST00000398213; ENSP00000381271; ENSG00000170473. [Q9BRP8-2]
ENST00000408946; ENSP00000386156; ENSG00000170473. [Q9BRP8-1]
GeneIDi84305.
KEGGihsa:84305.
UCSCiuc001sie.2. human. [Q9BRP8-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ459406 mRNA. Translation: CAD30677.1.
AK096922 mRNA. Translation: BAC04897.1.
AC023055 Genomic DNA. No translation available.
AC025162 Genomic DNA. No translation available.
BC006135 mRNA. Translation: AAH06135.1.
BC014976 mRNA. Translation: AAH14976.1.
CCDSiCCDS41795.1. [Q9BRP8-1]
CCDS44916.1. [Q9BRP8-2]
RefSeqiNP_001137325.1. NM_001143853.1. [Q9BRP8-2]
NP_115721.1. NM_032345.2. [Q9BRP8-1]
UniGeneiHs.505687.
Hs.524488.

3D structure databases

ProteinModelPortaliQ9BRP8.
SMRiQ9BRP8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124031. 76 interactors.
DIPiDIP-48413N.
IntActiQ9BRP8. 30 interactors.
MINTiMINT-3060675.
STRINGi9606.ENSP00000386156.

PTM databases

iPTMnetiQ9BRP8.
PhosphoSitePlusiQ9BRP8.

Polymorphism and mutation databases

BioMutaiWIBG.

Proteomic databases

EPDiQ9BRP8.
MaxQBiQ9BRP8.
PaxDbiQ9BRP8.
PeptideAtlasiQ9BRP8.
PRIDEiQ9BRP8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000398213; ENSP00000381271; ENSG00000170473. [Q9BRP8-2]
ENST00000408946; ENSP00000386156; ENSG00000170473. [Q9BRP8-1]
GeneIDi84305.
KEGGihsa:84305.
UCSCiuc001sie.2. human. [Q9BRP8-1]

Organism-specific databases

CTDi84305.
DisGeNETi84305.
GeneCardsiPYM1.
HGNCiHGNC:30258. PYM1.
HPAiCAB012803.
HPA039717.
HPA046200.
neXtProtiNX_Q9BRP8.
OpenTargetsiENSG00000170473.
PharmGKBiPA142670574.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4325. Eukaryota.
ENOG4111KHQ. LUCA.
GeneTreeiENSGT00730000111107.
HOGENOMiHOG000215176.
HOVERGENiHBG097451.
InParanoidiQ9BRP8.
KOiK14294.
OMAiKSAKRNM.
OrthoDBiEOG091G0XQ3.
PhylomeDBiQ9BRP8.
TreeFamiTF324615.

Miscellaneous databases

ChiTaRSiWIBG. human.
GenomeRNAii84305.
PROiPR:Q9BRP8.

Gene expression databases

BgeeiENSG00000170473.
CleanExiHS_WIBG.
ExpressionAtlasiQ9BRP8. baseline and differential.
GenevisibleiQ9BRP8. HS.

Family and domain databases

InterProiView protein in InterPro
IPR015362. WIBG_fam.
PfamiView protein in Pfam
PF09282. Mago-bind. 1 hit.
SMARTiView protein in SMART
SM01273. Mago-bind. 1 hit.
SUPFAMiSSF101931. SSF101931. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPYM1_HUMAN
AccessioniPrimary (citable) accession number: Q9BRP8
Secondary accession number(s): B6ZDM5, Q8IXJ8, Q8N8E7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 15, 2007
Last sequence update: June 1, 2001
Last modified: June 7, 2017
This is version 119 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. SIMILARITY comments
    Index of protein domains and families

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.