2yas

From Proteopedia

(Difference between revisions)

Current revision

HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE

Structural highlights

2yas is a 1 chain structure with sequence from Hevea brasiliensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.72Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HNL_HEVBR Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin.

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

The 3D structures of complexes between the hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL) and several substrate and/or inhibitor molecules, including trichloracetaldehyde, hexafluoracetone, acetone, and rhodanide, were determined by X-ray crystallography. The complex with trichloracetaldehyde showed a covalent linkage between the protein and the inhibitor, which had apparently resulted from nucleophilic attack of the catalytic Ser80-Ogamma. All other complexes showed the substrate or inhibitor molecule merely hydrogen bonded to the protein. In addition, the native crystal structure of Hb-HNL was redetermined at cryo-temperature and at room temperature, eliminating previous uncertainties concerning residual electron density within the active site, and leading to the observation of two conserved water molecules. One of them was found to be conserved in all complex structures and appears to have mainly structural significance. The other water molecule is conserved in all structures except for the complex with rhodanide; it is hydrogen bonded to the imidazole of the catalytic His235 and appears to affect the Hb-HNL catalyzed reaction. The observed 3D structural data suggest implications for the enzyme mechanism. It appears that the enzyme-catalyzed cyanohydrin formation is unlikely to proceed via a hemiacetal or hemiketal intermediate covalently attached to the enzyme, despite the observation of such an intermediate for the complex with trichloracetaldehyde. Instead, the data are consistent with a mechanism where the incoming substrate is activated by hydrogen bonding with its carbonyl oxygen to the Ser80 and Thr11 hydroxy groups. A hydrogen cyanide molecule subsequently replaces a water molecule and is deprotonated presumably by the His235 base. Deprotonation is facilitated by the proximity of the positive charge of the Lys236 side chain.

Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis.,Zuegg J, Gruber K, Gugganig M, Wagner UG, Kratky C Protein Sci. 1999 Oct;8(10):1990-2000. PMID:10548044^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Zuegg J, Gruber K, Gugganig M, Wagner UG, Kratky C. Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis. Protein Sci. 1999 Oct;8(10):1990-2000. PMID:10548044

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2yas"

Categories: Hevea brasiliensis | Large Structures | Gruber K | Gugganig M | Kratky C

@@ Line 1: / Line 1: @@
 ==HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE==
-<StructureSection load='2yas' size='340' side='right' caption='[[2yas]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+<StructureSection load='2yas' size='340' side='right'caption='[[2yas]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yas]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YAS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yas]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YAS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.72&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 Hevea brasiliensis])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxynitrilase Hydroxynitrilase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.37 4.1.2.37] </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=2yas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yas OCA], [https://pdbe.org/2yas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yas RCSB], [https://www.ebi.ac.uk/pdbsum/2yas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yas 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=2yas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yas OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yas RCSB], [http://www.ebi.ac.uk/pdbsum/2yas PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HNL_HEVBR HNL_HEVBR]] Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin.
+[https://www.uniprot.org/uniprot/HNL_HEVBR HNL_HEVBR] Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin.
 == 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/ya/2yas_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ya/2yas_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2yas ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2yas" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 33: / Line 34: @@
 </StructureSection>
 [[Category: Hevea brasiliensis]]
-[[Category: Hydroxynitrilase]]
+[[Category: Large Structures]]
-[[Category: Gruber, K]]
+[[Category: Gruber K]]
-[[Category: Gugganig, M]]
+[[Category: Gugganig M]]
-[[Category: Kratky, C]]
+[[Category: Kratky C]]
-[[Category: Cyanhydrin formation]]
-[[Category: Cyanogenesis]]
-[[Category: Lyase]]
-[[Category: Oxynitrilase]]

2yas

From Proteopedia

Current revision

HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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