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| - | [[Image:1a3c.jpg|left|200px]] | |
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| - | {{Structure
| + | ==PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC FORM== |
| - | |PDB= 1a3c |SIZE=350|CAPTION= <scene name='initialview01'>1a3c</scene>, resolution 1.6Å
| + | <StructureSection load='1a3c' size='340' side='right'caption='[[1a3c]], [[Resolution|resolution]] 1.60Å' scene=''> |
| - | |SITE= <scene name='pdbsite=PRA:Dual+Site+Binding+Site+For+Substrate+Prpp+In+This+And+Ot+...'>PRA</scene>, <scene name='pdbsite=SM1:Sm3++Ion+Binding+Site.+The+Sm3++Ion+Lies+On+A+Crystallog+...'>SM1</scene> and <scene name='pdbsite=SM2:Sm3++Ion+Binding+Site.+The+Sm3++Ion+Lies+On+A+General+Po+...'>SM2</scene>
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | + | <table><tr><td colspan='2'>[[1a3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A3C FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| - | |GENE= PYRR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1a3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a3c OCA], [https://pdbe.org/1a3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a3c RCSB], [https://www.ebi.ac.uk/pdbsum/1a3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a3c ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1a3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a3c OCA], [http://www.ebi.ac.uk/pdbsum/1a3c PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1a3c RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/PYRR_BACSU PYRR_BACSU] Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes.[HAMAP-Rule:MF_01219] Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.[HAMAP-Rule:MF_01219] |
| - | | + | == Evolutionary Conservation == |
| - | '''PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC FORM'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/1a3c_consurf.spt"</scriptWhenChecked> |
| - | BACKGROUND: The expression of pyrimidine nucleotide biosynthetic (pyr) genes in Bacillus subtilis is regulated by transcriptional attenuation. The PyrR attenuation protein binds to specific sites in pyr mRNA, allowing the formation of downstream terminator structures. UMP and 5-phosphoribosyl-1-pyrophosphate (PRPP), a nucleotide metabolite, are co-regulators with PyrR. The smallest RNA shown to bind tightly to PyrR is a 28-30 nucleotide stem-loop that contains a purine-rich bulge and a putative-GNRA tetraloop. PyrR is also a uracil phosphoribosyltransferase (UPRTase), although the relationship between enzymatic activity and RNA recognition is unclear, and the UPRTase activity of PyrR is not physiologically significant in B. subtilis. Elucidating the role of PyrR structural motifs in UMP-dependent RNA binding is an important step towards understanding the mechanism of pyr transcriptional attenuation. RESULTS: The 1.6 A crystal structure of B. subtilis PyrR has been determined by multiwavelength anomalous diffraction, using a Sm co-crystal. As expected, the structure of PyrR is homologous to those proteins of the large type I PRTase structural family; it is most similar to hypoxanthine-guanine-xanthine PRTase (HGXPRTase). The PyrR dimer differs from other PRTase dimers, suggesting it may have evolved specifically for RNA binding. A large, basic, surface at the dimer interface is an obvious RNA-binding site and uracil specificity is probably provided by hydrogen bonds from mainchain and sidechain atoms in the hood subdomain. These models of RNA and UMP binding are consistent with biological data. CONCLUSIONS: The B. subtilis protein PyrR has adapted the substrate- and product-binding capacities of a PRTase, probably an HGXPRTase, producing a new regulatory function in which the substrate and product are co-regulators of transcription termination. The structure is consistent with the idea that PyrR regulatory function is independent of catalytic activity, which is likely to be extremely low under physiological conditions.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1A3C is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A3C OCA].
| + | </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=1a3c ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | __TOC__ |
| - | Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase., Tomchick DR, Turner RJ, Switzer RL, Smith JL, Structure. 1998 Mar 15;6(3):337-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9551555 9551555]
| + | </StructureSection> |
| | [[Category: Bacillus subtilis]] | | [[Category: Bacillus subtilis]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Smith, J L.]] | + | [[Category: Smith JL]] |
| - | [[Category: Switzer, R W.]] | + | [[Category: Switzer RW]] |
| - | [[Category: Tomchick, D R.]] | + | [[Category: Tomchick DR]] |
| - | [[Category: Turner, R J.]] | + | [[Category: Turner RJ]] |
| - | [[Category: attenuation protein]]
| + | |
| - | [[Category: bifunctional enzyme]]
| + | |
| - | [[Category: phosphoribosyltransferase]]
| + | |
| - | [[Category: prtase]]
| + | |
| - | [[Category: pyrimidine biosynthesis]]
| + | |
| - | [[Category: rna-binding protein]]
| + | |
| - | [[Category: transcription regulation]]
| + | |
| - | [[Category: transferase]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:32:20 2008''
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