|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of Mycobacterium smegmatis AmtR== | | ==Crystal structure of Mycobacterium smegmatis AmtR== |
| - | <StructureSection load='5e57' size='340' side='right' caption='[[5e57]], [[Resolution|resolution]] 1.98Å' scene=''> | + | <StructureSection load='5e57' size='340' side='right'caption='[[5e57]], [[Resolution|resolution]] 1.98Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5e57]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E57 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5e57]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E57 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98Å</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=5e57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e57 OCA], [http://pdbe.org/5e57 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e57 RCSB], [http://www.ebi.ac.uk/pdbsum/5e57 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e57 ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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=5e57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e57 OCA], [https://pdbe.org/5e57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e57 RCSB], [https://www.ebi.ac.uk/pdbsum/5e57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e57 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A0R089_MYCS2 A0R089_MYCS2] |
| - | Soil-dwelling bacteria of the phylum actinomycetes generally harbor either GlnR or AmtR as global regulators of nitrogen metabolism. Mycobacterium smegmatis harbors both these canonical regulators; GlnR regulates the expression of key genes involved in nitrogen metabolism, while the function and signal transduction pathway of AmtR in M. smegmatis remains largely unknown. Here we report the structure and function of the M. smegmatis AmtR and describe the role of AmtR in the regulation of nitrogen metabolism in response to nitrogen availability. To determine the function of AmtR in M. smegmatis, we performed genome-wide expression profiling comparing the wild-type versus an amtR mutant and identified significant changes in the expression of 11 genes, including an operon involved in urea degradation. An AmtR-consensus binding motif (CTGTC-N4-GACAG) was identified in the promoter region of this operon and ligand-independent high-affinity AmtR binding was validated by both electrophoretic mobility shift assays and SPR measurements. We confirmed the transcription of a cis-encoded small RNA complementary to the gene encoding AmtR under nitrogen excess and propose a post-transcriptional regulatory mechanism for AmtR. The three-dimensional X-ray structure of AmtR at 2.0A revealed an overall TetR-like dimeric structure and alignment of the M. smegmatis AmtR and Corynebacterium glutamicum AmtR regulatory domains showed poor structural conservation providing a potential explanation for the lack of M. smegmatis AmtR interaction with the adenylylated PII protein. Taken together our data suggest an AmtR (repressor)/GlnR (activator) competitive binding mechanism for transcriptional regulation of urea metabolism that is controlled by a cis-encoded small antisense RNA.
| + | |
| - | | + | |
| - | Structure and function of AmtR in Mycobacterium smegmatis: Implications for post-transcriptional regulation of urea metabolism through a small antisense RNA.,Petridis M, Vickers C, Robson J, McKenzie JL, Bereza M, Sharrock A, Aung HL, Arcus VL, Cook GM J Mol Biol. 2016 Sep 15. pii: S0022-2836(16)30373-4. doi:, 10.1016/j.jmb.2016.09.009. PMID:27640309<ref>PMID:27640309</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5e57" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arcus, V L]] | + | [[Category: Large Structures]] |
| - | [[Category: McKenzie, J L]] | + | [[Category: Mycolicibacterium smegmatis MC2 155]] |
| - | [[Category: Vickers, C J]] | + | [[Category: Arcus VL]] |
| - | [[Category: Hth dna binding motif]] | + | [[Category: McKenzie JL]] |
| - | [[Category: Ligand binding domain]] | + | [[Category: Vickers CJ]] |
| - | [[Category: Nitrogen regulation]]
| + | |
| - | [[Category: Tetr]]
| + | |
| - | [[Category: Translation]]
| + | |
