4zc4

From Proteopedia

(Difference between revisions)

Revision as of 20:06, 5 August 2015

Crystal structure of LARP1-unique domain DM15

Structural highlights

4zc4 is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[LARP1_HUMAN] RNA-binding protein that promotes translation of specific classes of mRNAs downstream of the mTORC1 complex. Associates with the mRNA 5'cap in an MTOR-dependent manner and associates with mRNAs containing a 5' terminal oligopyrimidine (5'TOP) motif, which is present in mRNAs encoding for ribosomal proteins and several components of the translation machinery. Associates with actively translating ribosomes via interaction with PABPC1/PABP and stimulates translation of mRNAs containing a 5'TOP, thereby regulating cell growth and proliferation.^[1] ^[2] ^[3]

Publication Abstract from PubMed

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 A resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence.,Lahr RM, Mack SM, Heroux A, Blagden SP, Bousquet-Antonelli C, Deragon JM, Berman AJ Nucleic Acids Res. 2015 Jul 22. pii: gkv748. PMID:26206669^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Burrows C, Abd Latip N, Lam SJ, Carpenter L, Sawicka K, Tzolovsky G, Gabra H, Bushell M, Glover DM, Willis AE, Blagden SP. The RNA binding protein Larp1 regulates cell division, apoptosis and cell migration. Nucleic Acids Res. 2010 Sep;38(16):5542-53. doi: 10.1093/nar/gkq294. Epub 2010, Apr 29. PMID:20430826 doi:http://dx.doi.org/10.1093/nar/gkq294
↑ Aoki K, Adachi S, Homoto M, Kusano H, Koike K, Natsume T. LARP1 specifically recognizes the 3' terminus of poly(A) mRNA. FEBS Lett. 2013 Jul 11;587(14):2173-8. doi: 10.1016/j.febslet.2013.05.035. Epub, 2013 May 24. PMID:23711370 doi:http://dx.doi.org/10.1016/j.febslet.2013.05.035
↑ Tcherkezian J, Cargnello M, Romeo Y, Huttlin EL, Lavoie G, Gygi SP, Roux PP. Proteomic analysis of cap-dependent translation identifies LARP1 as a key regulator of 5'TOP mRNA translation. Genes Dev. 2014 Feb 15;28(4):357-71. doi: 10.1101/gad.231407.113. PMID:24532714 doi:http://dx.doi.org/10.1101/gad.231407.113
↑ Lahr RM, Mack SM, Heroux A, Blagden SP, Bousquet-Antonelli C, Deragon JM, Berman AJ. The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence. Nucleic Acids Res. 2015 Jul 22. pii: gkv748. PMID:26206669 doi:http://dx.doi.org/10.1093/nar/gkv748

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4zc4"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+==Crystal structure of LARP1-unique domain DM15==
+<StructureSection load='4zc4' size='340' side='right' caption='[[4zc4]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4zc4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZC4 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zc4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4zc4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zc4 PDBsum]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/LARP1_HUMAN LARP1_HUMAN]] RNA-binding protein that promotes translation of specific classes of mRNAs downstream of the mTORC1 complex. Associates with the mRNA 5'cap in an MTOR-dependent manner and associates with mRNAs containing a 5' terminal oligopyrimidine (5'TOP) motif, which is present in mRNAs encoding for ribosomal proteins and several components of the translation machinery. Associates with actively translating ribosomes via interaction with PABPC1/PABP and stimulates translation of mRNAs containing a 5'TOP, thereby regulating cell growth and proliferation.<ref>PMID:20430826</ref> <ref>PMID:23711370</ref> <ref>PMID:24532714</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 A resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.
-The entry 4zc4 is ON HOLD
+The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence.,Lahr RM, Mack SM, Heroux A, Blagden SP, Bousquet-Antonelli C, Deragon JM, Berman AJ Nucleic Acids Res. 2015 Jul 22. pii: gkv748. PMID:26206669<ref>PMID:26206669</ref>
-Authors: Lahr, R.M., Berman, A.J.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description:
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
-[[Category: Berman, A.J]]
+__TOC__
-[[Category: Lahr, R.M]]
+</StructureSection>
+[[Category: Berman, A J]]
+[[Category: Lahr, R M]]
+[[Category: Heat-like]]
+[[Category: Helical repeat]]
+[[Category: Mrna]]
+[[Category: Rna binding protein]]
+[[Category: Rna-binding]]

4zc4

From Proteopedia

Revision as of 20:06, 5 August 2015

Crystal structure of LARP1-unique domain DM15

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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