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3gdn

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[[Image:3gdn.png|left|200px]]
 
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==Almond hydroxynitrile lyase in complex with benzaldehyde==
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The line below this paragraph, containing "STRUCTURE_3gdn", creates the "Structure Box" on the page.
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<StructureSection load='3gdn' size='340' side='right'caption='[[3gdn]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3gdn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Prunus_dulcis Prunus dulcis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDN FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.67&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=HBX:BENZALDEHYDE'>HBX</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MXN:(2R)-HYDROXY(PHENYL)ETHANENITRILE'>MXN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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{{STRUCTURE_3gdn| PDB=3gdn | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gdn OCA], [https://pdbe.org/3gdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gdn RCSB], [https://www.ebi.ac.uk/pdbsum/3gdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gdn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MDL2_PRUDU MDL2_PRUDU] Involved in cyanogenesis, the release of HCN from injured tissues. Catalyzes the stereospecific addition of HCN to a variety of aldehydes in vitro. Has no oxidase activity. The redox properties of the FAD cofactor appear to be unimportant for catalysis.<ref>PMID:11566130</ref> <ref>PMID:6246955</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/3gdn_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3gdn ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In a large number of plant species hydroxynitrile lyases catalyse the decomposition of cyanohydrins in order to generate hydrogen cyanide upon tissue damage. Hydrogen cyanide serves as deterrent against herbivores and fungi. In vitro hydroxynitrile lyases are proficient biocatalysts for the stereospecific synthesis of cyanohydrins. Curiously, hydroxynitrile lyases from different species are completely unrelated in structure and substrate specificity despite catalysing the same reaction. The hydroxynitrile lyase from almond shows close resemblance to flavoproteins of the glucose-methanol-choline oxidoreductase family. We report here 3D structural data of this lyase with the reaction product benzaldehyde bound within the active site, which allow unambiguous assignment of the location of substrate binding. Based on the binding geometry, a reaction mechanism is proposed that involves one of the two conserved active site histidine residues acting as general base abstracting the proton from the cyanohydrin hydroxyl group. Site-directed mutagenesis shows that both active site histidines are required for the reaction to occur. There is no evidence that the flavin cofactor directly participates in the reaction. Comparison with other hydroxynitrile lyases reveals a large diversity of active site architectures, which, however, share the common features of a general active site base and a nearby patch with positive electrostatic potential. Based on the difference in substrate binding geometry between the FAD-dependent HNL from almond and the related oxidases we can rationalize why the HNL does not act as an oxidase.
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===Almond hydroxynitrile lyase in complex with benzaldehyde===
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Substrate Binding in the FAD-Dependent Hydroxynitrile Lyase from Almond Provides Insight into the Mechanism of Cyanohydrins Formation and Explains the Absence of Dehydrogenation Activity.,Dreveny I, Andryushkova A, Glieder A, Gruber K, Kratky C Biochemistry. 2009 Mar 3. PMID:19256550<ref>PMID:19256550</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19256550}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3gdn" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19256550 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19256550}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[3gdn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Prunus_dulcis Prunus dulcis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDN OCA].
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==Reference==
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<ref group="xtra">PMID:19256550</ref><ref group="xtra">PMID:11566130</ref><references group="xtra"/>
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[[Category: Mandelonitrile lyase]]
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[[Category: Prunus dulcis]]
[[Category: Prunus dulcis]]
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[[Category: Dreveny, I.]]
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[[Category: Dreveny I]]
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[[Category: Gruber, K.]]
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[[Category: Gruber K]]
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[[Category: Kratky, C.]]
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[[Category: Kratky C]]
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[[Category: Almond]]
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[[Category: Cyanogenesis]]
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[[Category: Flavin]]
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[[Category: Flavoprotein]]
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[[Category: Gmc oxidoreductase]]
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[[Category: Hydroxynitrile lyase]]
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[[Category: Lyase]]
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Current revision

Almond hydroxynitrile lyase in complex with benzaldehyde

PDB ID 3gdn

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