3wwp

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Current revision (08:47, 20 March 2024) (edit) (undo)
 
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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3wwp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Baliospermum_montanum Baliospermum montanum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WWP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WWP FirstGlance]. <br>
<table><tr><td colspan='2'>[[3wwp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Baliospermum_montanum Baliospermum montanum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WWP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WWP FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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]] 1.9&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wwo|3wwo]]</div></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=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bmhnl ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316758 Baliospermum montanum])</td></tr>
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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=3wwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wwp OCA], [https://pdbe.org/3wwp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wwp RCSB], [https://www.ebi.ac.uk/pdbsum/3wwp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wwp ProSAT]</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=3wwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wwp OCA], [https://pdbe.org/3wwp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wwp RCSB], [https://www.ebi.ac.uk/pdbsum/3wwp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wwp ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/D1MX73_9ROSI D1MX73_9ROSI]
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Hydroxynitrile lyases (HNLs) catalyze degradation of cyanohydrins to hydrogen cyanide and the corresponding ketone or aldehyde. HNLs can also catalyze the reverse reaction, i.e., synthesis of cyanohydrins. Although several crystal structures of S-selective hydroxynitrile lyases (S-HNLs) have been reported, it remains unknown whether and how dynamics at the active site of S-HNLs influence their broad substrate specificity and affinity. In this study, we analyzed the structure, dynamics and function of S-HNL from Baliospermum montanum (BmHNL), which has an alpha/beta hydrolase fold. Two crystal structures of BmHNL, apo1 and apo2, were determined at 2.55 and 1.9A, respectively. Structural comparison between BmHNL (apo2) and S-HNL from Hevea brasiliensis with (S)-mandelonitrile bound to the active site revealed that hydrophobic residues at the entrance region of BmHNL formed hydrophobic interactions with the benzene ring of the substrate. The flexible structures of these hydrophobic residues were confirmed by a 15ns molecular dynamics simulation. This flexibility regulated the size of the active site cavity, enabling binding of various substrates to BmHNL. The high affinity of BmHNL toward substrates containing a benzene ring was also confirmed by comparing the kinetics of BmHNL and S-HNL from Manihot esculenta. Taken together, the results indicated that the flexibility and placement of the residues are important for the broad substrate specificity of S-HNLs.
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Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics.,Nakano S, Dadashipour M, Asano Y Biochim Biophys Acta. 2014 Sep 16;1844(12):2059-2067. doi:, 10.1016/j.bbapap.2014.09.004. PMID:25220808<ref>PMID:25220808</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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<div class="pdbe-citations 3wwp" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Baliospermum montanum]]
[[Category: Baliospermum montanum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Asano, Y]]
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[[Category: Asano Y]]
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[[Category: Dadashipour, M]]
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[[Category: Dadashipour M]]
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[[Category: Nakano, S]]
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[[Category: Nakano S]]
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[[Category: Alpha/beta hydrolase fold]]
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[[Category: Lyase]]
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Current revision

S-selective hydroxynitrile lyase from Baliospermum montanum (apo2)

PDB ID 3wwp

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