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Protein

Y-box-binding protein 2

Gene

Ybx2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus promoter element. Binds to full length mRNA with high affinity in a sequence-independent manner. Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay.5 Publications

GO - Molecular functioni

  • chromatin binding Source: MGI
  • DNA binding Source: UniProtKB-KW
  • lipid binding Source: MGI
  • mRNA 3'-UTR binding Source: MGI
  • mRNA binding Source: MGI
  • ribonucleoprotein complex binding Source: MGI
  • translation regulator activity Source: MGI

GO - Biological processi

  • mRNA stabilization Source: MGI
  • negative regulation of binding Source: MGI
  • negative regulation of translation Source: MGI
  • oogenesis Source: MGI
  • regulation of transcription, DNA-templated Source: InterPro
  • spermatid development Source: MGI
Complete GO annotation...

Keywords - Ligandi

DNA-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Y-box-binding protein 2
Alternative name(s):
FRGY2 homolog
Germ cell-specific Y-box-binding protein
Gene namesi
Name:Ybx2
Synonyms:Msy2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1096372. Ybx2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • intracellular ribonucleoprotein complex Source: MGI
  • nucleolus Source: MGI
  • polysome Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi109 – 1091Y → A: Abolishes cytoplasmic retention and mRNA-binding affinity; when associated with A-111. 1 Publication
Mutagenesisi111 – 1111F → A: Abolishes cytoplasmic retention and mRNA-binding affinity; when associated with A-109. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 360360Y-box-binding protein 2PRO_0000100226Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei67 – 671PhosphothreonineCombined sources
Modified residuei78 – 781PhosphothreonineCombined sources
Modified residuei252 – 2521PhosphoserineCombined sources

Post-translational modificationi

Phosphorylated during oocyte maturation and dephosphorylated following egg activation. Phosphorylated in vitro by a kinase activity associated with testicular mRNPs. Dephosphorylation leads to a decrease in its affinity to bind RNA in vitro.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9Z2C8.
MaxQBiQ9Z2C8.
PaxDbiQ9Z2C8.
PeptideAtlasiQ9Z2C8.
PRIDEiQ9Z2C8.

2D gel databases

REPRODUCTION-2DPAGEQ9Z2C8.

PTM databases

iPTMnetiQ9Z2C8.
PhosphoSiteiQ9Z2C8.

Expressioni

Tissue specificityi

Expressed in meiotic and postmeiotic male germ cells and oocytes; poorly expressed in two cell stage embryos (at protein level). Not detected in preimplantation embryos.2 Publications

Gene expression databases

BgeeiQ9Z2C8.
CleanExiMM_YBX2.

Interactioni

Subunit structurei

Found in a mRNP complex with PABPC1 and YBX3.2 Publications

Protein-protein interaction databases

DIPiDIP-59783N.
STRINGi10090.ENSMUSP00000018698.

Structurei

3D structure databases

ProteinModelPortaliQ9Z2C8.
SMRiQ9Z2C8. Positions 89-166.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini95 – 16571CSDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni89 – 17183Required for cytoplasmic retentionAdd
BLAST
Regioni219 – 360142Required for mRNA-bindingAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi41 – 5717Gly-richAdd
BLAST
Compositional biasi174 – 24168Arg-richAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG079361.
InParanoidiQ9Z2C8.
PhylomeDBiQ9Z2C8.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9Z2C8-1) [UniParc]FASTAAdd to basket

Also known as: Msy2

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
MSEAEASVVA TAAPAATVPA TAAGVVAVVV PVPAGEPQKA GGGAGGGGGA
60 70 80 90 100
ASGPAAGTPL HAPGPRTPGN QATAASGTPA PPARSQADKP VLAIQVLGTV
110 120 130 140 150
KWFNVRNGYG FINRNDTKED VFVHQTAIKR NNPRKFLRSV GDGETVEFDV
160 170 180 190 200
VEGEKGARAA NVTGPGGVPV KGSRYAPNRR RFRRFIPRPR PAAPPPMVAE
210 220 230 240 250
APSGGTEPGS EGERAEDSGQ RPRRRRPPPF FYRRRFVRGP RPPNQQQPIE
260 270 280 290 300
GSDGVEPKET APLEGDQQQG DERVPPPRFR PRYRRPFRPR PPQQPTTEGG
310 320 330 340 350
DGETKPSQGP TDGSRPEPQR PRNRPYFQRR RQQPPGPRQP IAAETSAPIN
360
SGDPPTTILE
Length:360
Mass (Da):38,271
Last modified:May 1, 1999 - v1
Checksum:iDFCAAE7F936731BF
GO
Isoform 2 (identifier: Q9Z2C8-2) [UniParc]FASTAAdd to basket

Also known as: Msy2a

The sequence of this isoform differs from the canonical sequence as follows:
     1-78: Missing.
     79-91: PAPPARSQADKPV → MSRRAGQAGSAKA

Note: In Ref.4 isoform 2 not detected in oocytes.
Show »
Length:282
Mass (Da):31,465
Checksum:i4C19AF0EDC9CDEF2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti60 – 612LH → S in CAI35155 (PubMed:19468303).Curated
Sequence conflicti158 – 1581R → E in CAI35155 (PubMed:19468303).Curated
Sequence conflicti158 – 1581R → E in CAI35156 (PubMed:19468303).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 7878Missing in isoform 2. 1 PublicationVSP_013052Add
BLAST
Alternative sequencei79 – 9113PAPPA…ADKPV → MSRRAGQAGSAKA in isoform 2. 1 PublicationVSP_013053Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF073954 mRNA. Translation: AAC98673.1.
AF073955 mRNA. Translation: AAC98674.1.
AL596185 Genomic DNA. Translation: CAI35155.1.
AL596185 Genomic DNA. Translation: CAI35156.1.
UniGeneiMm.29286.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF073954 mRNA. Translation: AAC98673.1.
AF073955 mRNA. Translation: AAC98674.1.
AL596185 Genomic DNA. Translation: CAI35155.1.
AL596185 Genomic DNA. Translation: CAI35156.1.
UniGeneiMm.29286.

3D structure databases

ProteinModelPortaliQ9Z2C8.
SMRiQ9Z2C8. Positions 89-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59783N.
STRINGi10090.ENSMUSP00000018698.

PTM databases

iPTMnetiQ9Z2C8.
PhosphoSiteiQ9Z2C8.

2D gel databases

REPRODUCTION-2DPAGEQ9Z2C8.

Proteomic databases

EPDiQ9Z2C8.
MaxQBiQ9Z2C8.
PaxDbiQ9Z2C8.
PeptideAtlasiQ9Z2C8.
PRIDEiQ9Z2C8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Organism-specific databases

MGIiMGI:1096372. Ybx2.

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG079361.
InParanoidiQ9Z2C8.
PhylomeDBiQ9Z2C8.

Miscellaneous databases

ChiTaRSiYbx2. mouse.
PROiQ9Z2C8.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Z2C8.
CleanExiMM_YBX2.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Mammalian male and female germ cells express a germ cell-specific Y-box protein, MSY2."
    Gu W., Tekur S., Reinbold R., Eppig J.J., Choi Y.-C., Zheng J.Z., Murray M.T., Hecht N.B.
    Biol. Reprod. 59:1266-1274(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY.
    Strain: CD-1.
    Tissue: Testis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "The mouse Y-box protein, MSY2, is associated with a kinase on non-polysomal mouse testicular mRNAs."
    Herbert T.P., Hecht N.B.
    Nucleic Acids Res. 27:1747-1753(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MRNA TRANSLATION, PHOSPHORYLATION, RNA-BINDING, IDENTIFICATION IN A MRNP COMPLEX WITH PABPC1.
  4. "A sequence-specific RNA binding complex expressed in murine germ cells contains MSY2 and MSY4."
    Davies H.G., Giorgini F., Fajardo M.A., Braun R.E.
    Dev. Biol. 221:87-100(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A MRNP COMPLEX WITH YBX3.
    Tissue: Testis.
  5. "Expression of MSY2 in mouse oocytes and preimplantation embryos."
    Yu J., Hecht N.B., Schultz R.M.
    Biol. Reprod. 65:1260-1270(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  6. "MSY2 and MSY4 bind a conserved sequence in the 3' untranslated region of protamine 1 mRNA in vitro and in vivo."
    Giorgini F., Davies H.G., Braun R.E.
    Mol. Cell. Biol. 21:7010-7019(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: RNA-BINDING.
  7. "RNA-binding properties and translation repression in vitro by germ cell-specific MSY2 protein."
    Yu J., Hecht N.B., Schultz R.M.
    Biol. Reprod. 67:1093-1098(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MRNA TRANSLATION, RNA-BINDING.
  8. "Requirement for RNA-binding activity of MSY2 for cytoplasmic localization and retention in mouse oocytes."
    Yu J., Hecht N.B., Schultz R.M.
    Dev. Biol. 255:249-262(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MATERNAL MRNA CYTOPLASMIC RETENTION, RNA-BINDING, MUTAGENESIS OF TYR-109 AND PHE-111.
  9. "Transgenic RNAi-mediated reduction of MSY2 in mouse oocytes results in reduced fertility."
    Yu J., Deng M., Medvedev S., Yang J., Hecht N.B., Schultz R.M.
    Dev. Biol. 268:195-206(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MRNA STABILITY.
  10. "The DNA/RNA-binding protein MSY2 marks specific transcripts for cytoplasmic storage in mouse male germ cells."
    Yang J., Medvedev S., Reddi P.P., Schultz R.M., Hecht N.B.
    Proc. Natl. Acad. Sci. U.S.A. 102:1513-1518(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN CYTOPLASMIC MRNA STORAGE, RNA-BINDING, DNA-BINDING.
  11. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-67; THR-78 AND SER-252, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brown adipose tissue, Heart and Testis.

Entry informationi

Entry nameiYBOX2_MOUSE
AccessioniPrimary (citable) accession number: Q9Z2C8
Secondary accession number(s): Q5NCW8, Q5NCW9, Q9Z2C7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: May 1, 1999
Last modified: July 6, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Knockout mice for this gene exhibited reduced level of mRNA and protein synthesis in fully grown oocytes and decrease fertility.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.