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==Alkalihalobacillus halodurans (Aha) trp RNA binding attenuation protein (TRAP) mutant dTRAP with Trp==
<StructureSection load='9bds' size='340' side='right'caption='[[9bds]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9bds]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9BDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9BDS FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></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=9bds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9bds OCA], [https://pdbe.org/9bds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9bds RCSB], [https://www.ebi.ac.uk/pdbsum/9bds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9bds ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MTRB_HALH5 MTRB_HALH5] Required for transcription attenuation control in the Trp operon. This trans-acting factor seems to recognize a 10 bases nucleotide sequence in the Trp leader transcript causing transcription termination. Binds the leader RNA only in presence of L-tryptophan (By similarity).
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== Publication Abstract from PubMed ==
The homo-dodecameric ring-shaped trp RNA binding attenuation protein (TRAP) from Alkalihalobacillus halodurans (Aha) binds up to twelve tryptophan ligands (Trp) and becomes activated to bind a specific sequence in the 5' leader region of the trp operon mRNA, thereby downregulating biosynthesis of Trp. Thermodynamic measurements of Trp binding have revealed a range of cooperative behavior for different TRAP variants, even if the averaged apparent affinities for Trp have been found to be similar. Proximity between the ligand binding sites, and the ligand-coupled disorder-to-order transition has implicated nearest-neighbor interactions in cooperativity. To establish a solid basis for describing nearest-neighbor cooperativity in TRAP, we engineered variants constructed with two subunits connected by a flexible linker (dTRAP). We mutated the binding sites of alternating protomers such that only every other site was competent for Trp binding (WT-Mut dTRAP). Ligand binding monitored by NMR, calorimetry, and native mass spectrometry revealed strong cooperativity in dTRAP containing adjacent binding-competent sites, but a severe binding defect when the wild-type sites were separated by mutated sites. Cryo-EM experiments of dTRAP in its ligand-free apo state, and both dTRAP and WT-Mut dTRAP in the presence of Trp, revealed progressive stabilization of loops that gate the Trp binding site and participate in RNA binding. These studies provide important insights into the thermodynamic and structural basis for the observed ligand binding cooperativity in TRAP. Such insights can be useful for understanding allosteric control networks and for the development of those with defined ligand sensitivity and regulatory control.

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM.,Li W, Yang H, Stachowski K, Norris AS, Lichtenthal K, Kelly S, Gollnick P, Wysocki VH, Foster MP Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2409030121. doi: , 10.1073/pnas.2409030121. Epub 2024 Dec 30. PMID:39793047<ref>PMID:39793047</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Alkalihalobacillus halodurans]]
[[Category: Large Structures]]
[[Category: Foster M]]
[[Category: Stachowski K]]
[[Category: Yang H]]