1duv: Difference between revisions

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-[[Image:1duv.jpg|left|200px]]<br /><applet load="1duv" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1duv, resolution 1.7&Aring;" />
-'''CRYSTAL STRUCTURE OF E. COLI ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH NDELTA-L-ORNITHINE-DIAMINOPHOSPHINYL-N-SULPHONIC ACID (PSORN)'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF E. COLI ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH NDELTA-L-ORNITHINE-DIAMINOPHOSPHINYL-N-SULPHONIC ACID (PSORN)==
-The crystal structure is reported at 1.8 A resolution of Escherichia coli ornithine transcarbamoylase in complex with the active derivative of phaseolotoxin from Pseudomonas syringae pv. phaseolicola, N(delta)-(N'-sulfodiaminophosphinyl)-l-ornithine. Electron density reveals that the complex is not a covalent adduct as previously thought. Kinetic data confirm that N(delta)-(N'-sulfodiaminophosphinyl)-l-ornithine exhibits reversible inhibition with a half-life in the order of approximately 22 h and a dissociation constant of K(D) = 1.6 x 10(-12) m at 37 degrees C and pH 8.0. Observed hydrogen bonding about the chiral tetrahedral phosphorus of the inhibitor is consistent only with the presence of the R enantiomer. A strong interaction is also observed between Arg(57) Nepsilon and the P-N-S bridging nitrogen indicating that imino tautomers of N(delta)-(N'-sulfodiaminophosphinyl)-l-ornithine are present in the bound state. An imino tautomer of N(delta)-(N'-sulfodiaminophosphinyl)-l-ornithine is structurally analogous to the proposed reaction transition state. Hence, we propose that N(delta)-(N'-sulfodiaminophosphinyl)-l-ornithine, with its three unique N-P bonds, represents a true transition state analogue for ornithine transcarbamoylases, consistent with the tight binding kinetics observed.
+<StructureSection load='1duv' size='340' side='right'caption='[[1duv]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1duv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DUV FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PSQ:NDELTA-(N-SULPHODIAMINOPHOSPHINYL)-L-ORNITHINE'>PSQ</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=1duv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1duv OCA], [https://pdbe.org/1duv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1duv RCSB], [https://www.ebi.ac.uk/pdbsum/1duv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1duv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OTC1_ECOLI OTC1_ECOLI] Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline, which is a substrate for argininosuccinate synthetase, the enzyme involved in the final step in arginine biosynthesis.<ref>PMID:3072022</ref> <ref>PMID:789338</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/1duv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1duv ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-DUV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=PSQ:'>PSQ</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ornithine_carbamoyltransferase Ornithine carbamoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.3 2.1.3.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DUV OCA].
+*[[Ornithine carbamoyltransferase 3D structures|Ornithine carbamoyltransferase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Mechanism of inactivation of ornithine transcarbamoylase by Ndelta -(N'-Sulfodiaminophosphinyl)-L-ornithine, a true transition state analogue? Crystal structure and implications for catalytic mechanism., Langley DB, Templeton MD, Fields BA, Mitchell RE, Collyer CA, J Biol Chem. 2000 Jun 30;275(26):20012-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10747936 10747936]
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Ornithine carbamoyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Collyer CA]]
-[[Category: Collyer, C A.]]
+[[Category: Fields BA]]
-[[Category: Fields, B A.]]
+[[Category: Langley DB]]
-[[Category: Langley, D B.]]
+[[Category: Mitchell RE]]
-[[Category: Mitchell, R E.]]
+[[Category: Templeton MD]]
-[[Category: Templeton, M D.]]
-[[Category: MPD]]
-[[Category: PSQ]]
-[[Category: enzyme-inhibitor complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:20:50 2008''