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==SOLUTION STRUCTURE OF THE NUCLEAR FACTOR ALY RBD DOMAIN==
==SOLUTION STRUCTURE OF THE NUCLEAR FACTOR ALY RBD DOMAIN==
<StructureSection load='1no8' size='340' side='right'caption='[[1no8]], [[NMR_Ensembles_of_Models | 32 NMR models]]' scene=''>
<StructureSection load='1no8' size='340' side='right'caption='[[1no8]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1no8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NO8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1no8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NO8 FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ALY ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1no8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1no8 OCA], [https://pdbe.org/1no8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1no8 RCSB], [https://www.ebi.ac.uk/pdbsum/1no8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1no8 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1no8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1no8 OCA], [https://pdbe.org/1no8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1no8 RCSB], [https://www.ebi.ac.uk/pdbsum/1no8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1no8 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/THOC4_MOUSE THOC4_MOUSE]] Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex (By similarity).<ref>PMID:9119228</ref> <ref>PMID:10786854</ref>  Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Plays a role in mRNA processing and export. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay (By similarity).<ref>PMID:9119228</ref> <ref>PMID:10786854</ref>
[https://www.uniprot.org/uniprot/THOC4_MOUSE THOC4_MOUSE] Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex (By similarity).<ref>PMID:9119228</ref> <ref>PMID:10786854</ref>  Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Plays a role in mRNA processing and export. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay (By similarity).<ref>PMID:9119228</ref> <ref>PMID:10786854</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1no8 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1no8 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
ALY is a ubiquitously expressed nuclear protein which interacts with proteins such as TAP that are involved in export of mRNA from the nucleus to the cytoplasm, as well as with proteins that bind the T cell receptor alpha gene enhancer. ALY has also been shown to bind mRNA and to co-localize in the nucleus with components of a multiprotein postsplicing complex that is deposited 20-24 nucleotides upstream of exon-exon junctions. ALY has a conserved RNA binding domain (RBD) flanked by Gly-Arg rich N-terminal and C-terminal sequences. We determined the solution structure of the RBD homology region in ALY by nuclear magnetic resonance methods. The RBD motif in ALY has a characteristic beta(1)alpha(1)beta(2)-beta(3)alpha(2)beta(4) fold, consisting of a beta sheet composed of four antiparallel beta strands and two alpha helices that pack on one face of the beta sheet. As in other RBD structures, the beta sheet has an exposed face with hydrophobic and charged residues that could modulate interactions with other molecules. The loop that connects beta strands 2 and 3 is in intermediate motion in the NMR time scale, which is also characteristic of other RBDs. This loop presents side chains close to the exposed surface of the beta sheet and is a primary candidate site for intermolecular interactions. The structure of the conserved RBD of ALY provides insight into the nature of interactions involving this multifunctional protein.
Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.,Perez-Alvarado GC, Martinez-Yamout M, Allen MM, Grosschedl R, Dyson HJ, Wright PE Biochemistry. 2003 Jun 24;42(24):7348-57. PMID:12809490<ref>PMID:12809490</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1no8" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lk3 transgenic mice]]
[[Category: Mus musculus]]
[[Category: Allen, M M]]
[[Category: Allen MM]]
[[Category: Dyson, H J]]
[[Category: Dyson HJ]]
[[Category: Grosschedl, R]]
[[Category: Grosschedl R]]
[[Category: Martinez-Yamout, M]]
[[Category: Martinez-Yamout M]]
[[Category: Perez-Alvarado, G C]]
[[Category: Perez-Alvarado GC]]
[[Category: Wright, P E]]
[[Category: Wright PE]]
[[Category: Aly]]
[[Category: Bef]]
[[Category: Mrna export factor]]
[[Category: Rbd]]
[[Category: Ref1-i]]
[[Category: Rna binding protein]]

Revision as of 11:51, 10 April 2024

SOLUTION STRUCTURE OF THE NUCLEAR FACTOR ALY RBD DOMAINSOLUTION STRUCTURE OF THE NUCLEAR FACTOR ALY RBD DOMAIN

Structural highlights

1no8 is a 1 chain structure with sequence from Mus musculus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

THOC4_MOUSE Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex (By similarity).[1] [2] Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Plays a role in mRNA processing and export. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay (By similarity).[3] [4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Bruhn L, Munnerlyn A, Grosschedl R. ALY, a context-dependent coactivator of LEF-1 and AML-1, is required for TCRalpha enhancer function. Genes Dev. 1997 Mar 1;11(5):640-53. PMID:9119228
  2. ↑ Stutz F, Bachi A, Doerks T, Braun IC, Seraphin B, Wilm M, Bork P, Izaurralde E. REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA. 2000 Apr;6(4):638-50. PMID:10786854
  3. ↑ Bruhn L, Munnerlyn A, Grosschedl R. ALY, a context-dependent coactivator of LEF-1 and AML-1, is required for TCRalpha enhancer function. Genes Dev. 1997 Mar 1;11(5):640-53. PMID:9119228
  4. ↑ Stutz F, Bachi A, Doerks T, Braun IC, Seraphin B, Wilm M, Bork P, Izaurralde E. REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA. 2000 Apr;6(4):638-50. PMID:10786854
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