1raa: Difference between revisions

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-[[Image:1raa.gif|left|200px]]<br /><applet load="1raa" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1raa, resolution 2.5&Aring;" />
-'''CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY==
-The X-ray crystal structure of CTP-ligated T state aspartate, transcarbamoylase has been refined to an R factor of 0.182 at 2.5 A, resolution using the computer program X-PLOR. The structure contains 81, sites for solvent and has rms deviations from ideality in bond lengths and, bond angles of 0.018 A and 3.722 degrees, respectively. The cytosine base, of CTP interacts with the main chain carbonyl oxygens of rTyr-89 and, rIle-12, the main chain NH of rIle-12, and the amino group of rLys-60. The, ribose hydroxyls form polar contacts with the amino group of rLys-60, a, carboxylate oxygen of rAsp-19, and the main chain carbonyl oxygen of, rVal-9. The phosphate oxygens of CTP interact with the amino group of, rLys-94, the hydroxyl of rThr-82, and an imidazole nitrogen of rHis-20., Recent mutagenesis experiments evaluated in parallel with the structure, reported here indicate that alterations in the hydrogen bonding, environment of the side chain of rAsn-111 may be responsible for the, homotropic behavior of the pAR5 mutant of ATCase. The location of the, first seven residues of the regulatory chain has been identified for the, first time in a refined ATCase crystal structure, and the proximity of, this portion of the regulatory chain to the allosteric site suggests a, potential role for these residues in nucleotide binding to the enzyme., Finally, a series of amino acid side chain rearrangements leading from the, R1 CTP allosteric to the R6 CTP allosteric site has been identified which, may constitute the molecular mechanism of distinct CTP binding sites on, ATCase.
+<StructureSection load='1raa' size='340' side='right'caption='[[1raa]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1raa]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RAA 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1raa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1raa OCA], [https://pdbe.org/1raa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1raa RCSB], [https://www.ebi.ac.uk/pdbsum/1raa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1raa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRB_ECOLI PYRB_ECOLI]
+== 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/ra/1raa_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=1raa ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-RAA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN and CTP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspartate_carbamoyltransferase Aspartate carbamoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.2 2.1.3.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RAA OCA].
+*[[Aspartate carbamoyltransferase 3D structures|Aspartate carbamoyltransferase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for ATCase mutants and the mechanism of negative cooperativity., Kosman RP, Gouaux JE, Lipscomb WN, Proteins. 1993 Feb;15(2):147-76. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8441751 8441751]
+[[Category: Escherichia coli K-12]]
-[[Category: Aspartate carbamoyltransferase]]
+[[Category: Large Structures]]
-[[Category: Escherichia coli]]
+[[Category: Gouaux JE]]
-[[Category: Protein complex]]
+[[Category: Kosman RP]]
-[[Category: Gouaux, J.E.]]
+[[Category: Lipscomb WN]]
-[[Category: Kosman, R.P.]]
-[[Category: Lipscomb, W.N.]]
-[[Category: CTP]]
-[[Category: ZN]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:23:43 2007''