1tz2: Difference between revisions
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==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]] 2.10Å' scene=''> | <StructureSection load='1tz2' size='340' side='right'caption='[[1tz2]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1tz2]] is a 4 chain structure with sequence from [ | <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=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | ||
<tr id=' | <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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/1A1D_PSEUD 1A1D_PSEUD] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tz/1tz2_consurf.spt"</scriptWhenChecked> | <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> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1tz2" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Deaminase|Deaminase]] | *[[Deaminase 3D structures|Deaminase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Pseudomonas sp]] | [[Category: Pseudomonas sp. ACP]] | ||
[[Category: Kao | [[Category: Kao CL]] | ||
[[Category: Karthikeyan | [[Category: Karthikeyan S]] | ||
[[Category: Liu | [[Category: Liu HW]] | ||
[[Category: Robinson | [[Category: Robinson H]] | ||
[[Category: Tao | [[Category: Tao Z]] | ||
[[Category: Zhang | [[Category: Zhang H]] | ||
[[Category: Zhao | [[Category: Zhao Z]] | ||
[[Category: Zhou | [[Category: Zhou Q]] | ||
Latest revision as of 09:35, 23 August 2023
Crystal structure of 1-aminocyclopropane-1-carboyxlate deaminase complexed with ACCCrystal structure of 1-aminocyclopropane-1-carboyxlate deaminase complexed with ACC
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed1-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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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