1tz2: Difference between revisions

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-[[Image:1tz2.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1tz2", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
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-{{STRUCTURE_1tz2|  PDB=1tz2  |  SCENE=  }}
-'''Crystal structure of 1-aminocyclopropane-1-carboyxlate deaminase complexed with ACC'''
+==Crystal structure of 1-aminocyclopropane-1-carboyxlate deaminase complexed with ACC==
+<StructureSection load='1tz2' size='340' side='right'caption='[[1tz2]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1tz2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._ACP Pseudomonas sp. ACP]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TZ2 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]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1AC:1-AMINOCYCLOPROPANECARBOXYLIC+ACID'>1AC</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=1tz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tz2 OCA], [https://pdbe.org/1tz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tz2 RCSB], [https://www.ebi.ac.uk/pdbsum/1tz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tz2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/1A1D_PSEUD 1A1D_PSEUD]
+== 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/tz/1tz2_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=1tz2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+-Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is retained in the product. How the reaction is initiated to generate an alpha-carbanionic intermediate, which is the common entry for most PLP-dependent reactions, is not obvious. To gain insight into this unusual ring-opening reaction, we have solved the crystal structures of ACC deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product alpha-ketobutyrate, and two d-amino acids. Several notable observations of these structural studies include the following: (1) a typically elusive gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP; (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of ACC in the gem-diamine complexes, implicating a direct role of this residue in the ring-opening reaction; (3) Tyr294 may also be responsible for the abstraction of the alpha-proton from d-amino acids, a prelude to the subsequent deamination reaction; (4) the steric hindrance precludes accessibility of active site functional groups to the l-amino acid substrates and may account for the stereospecificity of this enzyme toward d-amino acids. These structural data provide evidence favoring a mechanism in which the ring cleavage is induced by a nucleophilic attack at the pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile. However, these observations are also consistent with an alternative mechanistic possibility in which the ring opening is acid-catalyzed and may be facilitated by charge relay through PLP, where Tyr294 functions as a general acid. The results of mutagenesis studies corroborated the assigned critical role for Tyr294 in the catalysis.
-==Overview==
+Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: insight into the mechanism of a unique pyridoxal-5'-phosphate dependent cyclopropane ring-opening reaction.,Karthikeyan S, Zhou Q, Zhao Z, Kao CL, Tao Z, Robinson H, Liu HW, Zhang H Biochemistry. 2004 Oct 26;43(42):13328-39. PMID:15491139<ref>PMID:15491139</ref>
--Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is retained in the product. How the reaction is initiated to generate an alpha-carbanionic intermediate, which is the common entry for most PLP-dependent reactions, is not obvious. To gain insight into this unusual ring-opening reaction, we have solved the crystal structures of ACC deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product alpha-ketobutyrate, and two d-amino acids. Several notable observations of these structural studies include the following: (1) a typically elusive gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP; (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of ACC in the gem-diamine complexes, implicating a direct role of this residue in the ring-opening reaction; (3) Tyr294 may also be responsible for the abstraction of the alpha-proton from d-amino acids, a prelude to the subsequent deamination reaction; (4) the steric hindrance precludes accessibility of active site functional groups to the l-amino acid substrates and may account for the stereospecificity of this enzyme toward d-amino acids. These structural data provide evidence favoring a mechanism in which the ring cleavage is induced by a nucleophilic attack at the pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile. However, these observations are also consistent with an alternative mechanistic possibility in which the ring opening is acid-catalyzed and may be facilitated by charge relay through PLP, where Tyr294 functions as a general acid. The results of mutagenesis studies corroborated the assigned critical role for Tyr294 in the catalysis.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-TZ2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TZ2 OCA].
+</div>
+<div class="pdbe-citations 1tz2" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: insight into the mechanism of a unique pyridoxal-5'-phosphate dependent cyclopropane ring-opening reaction., Karthikeyan S, Zhou Q, Zhao Z, Kao CL, Tao Z, Robinson H, Liu HW, Zhang H, Biochemistry. 2004 Oct 26;43(42):13328-39. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15491139 15491139]
+*[[Deaminase 3D structures|Deaminase 3D structures]]
-[[Category: 1-aminocyclopropane-1-carboxylate deaminase]]
+== References ==
-[[Category: Pseudomonas sp.]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Kao, C L.]]
+</StructureSection>
-[[Category: Karthikeyan, S.]]
+[[Category: Large Structures]]
-[[Category: Liu, H W.]]
+[[Category: Pseudomonas sp. ACP]]
-[[Category: Robinson, H.]]
+[[Category: Kao CL]]
-[[Category: Tao, Z.]]
+[[Category: Karthikeyan S]]
-[[Category: Zhang, H.]]
+[[Category: Liu HW]]
-[[Category: Zhao, Z.]]
+[[Category: Robinson H]]
-[[Category: Zhou, Q.]]
+[[Category: Tao Z]]
-[[Category: Acc]]
+[[Category: Zhang H]]
-[[Category: Accd]]
+[[Category: Zhao Z]]
-[[Category: Complex]]
+[[Category: Zhou Q]]
-[[Category: Crystal]]
-[[Category: Plp]]
-[[Category: Structure]]
-[[Category: Substrate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 10:32:32 2008''