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| | ==Hydroxynitrile lyase from almond, monoclinic crystal form== | | ==Hydroxynitrile lyase from almond, monoclinic crystal form== |
| - | <StructureSection load='3gdp' size='340' side='right' caption='[[3gdp]], [[Resolution|resolution]] 1.57Å' scene=''> | + | <StructureSection load='3gdp' size='340' side='right'caption='[[3gdp]], [[Resolution|resolution]] 1.57Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3gdp]] 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=3GDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GDP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3gdp]] 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=3GDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.57Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ju2|1ju2]], [[3gdn|3gdn]]</td></tr>
| + | <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=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(R)-mandelonitrile_lyase (R)-mandelonitrile lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.10 4.1.2.10] </span></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=3gdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gdp OCA], [https://pdbe.org/3gdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gdp RCSB], [https://www.ebi.ac.uk/pdbsum/3gdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gdp ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gdp OCA], [http://pdbe.org/3gdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gdp RCSB], [http://www.ebi.ac.uk/pdbsum/3gdp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gdp ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/3gdp_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/3gdp_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Prunus dulcis]] | | [[Category: Prunus dulcis]] |
| - | [[Category: Dreveny, I]] | + | [[Category: Dreveny I]] |
| - | [[Category: Gruber, K]] | + | [[Category: Gruber K]] |
| - | [[Category: Kratky, C]] | + | [[Category: Kratky C]] |
| - | [[Category: Almond]]
| + | |
| - | [[Category: Cyanogenesis]]
| + | |
| - | [[Category: Flavin]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Gmc oxidoreductase]]
| + | |
| - | [[Category: Hydroxynitrile lyase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
3gdp is a 2 chain structure with sequence from Prunus dulcis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.57Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dreveny I, Gruber K, Glieder A, Thompson A, Kratky C. The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase. Structure. 2001 Sep;9(9):803-15. PMID:11566130
- ↑ Jorns MS. Studies on the kinetics of cyanohydrin synthesis and cleavage by the the flavoenzyme oxynitrilase. Biochim Biophys Acta. 1980;613(1):203-9. PMID:6246955
- ↑ Dreveny I, Andryushkova A, Glieder A, Gruber K, Kratky C. 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. Biochemistry. 2009 Mar 3. PMID:19256550 doi:10.1021/bi802162s
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