2hor

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of alliinase from garlic- apo form

Structural highlights

2hor is a 1 chain structure with sequence from Allium sativum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ALLN1_ALLSA Able to cleave the C-S bond of sulfoxide derivatives of Cys to produce allicin, thus giving rise to all sulfur compounds which are responsible for most of the properties of garlic, such as the specific smell and flavor as well as the health benefits like blood lipid or blood pressure lowering.

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

Alliinase (alliin lyase EC 4.4.1.4), a PLP-dependent alpha, beta-eliminating lyase, constitutes one of the major protein components of garlic (Alliium sativum L.) bulbs. The enzyme is a homodimeric glycoprotein and catalyzes the conversion of a specific non-protein sulfur-containing amino acid alliin ((+S)-allyl-L-cysteine sulfoxide) to allicin (diallyl thiosulfinate, the well known biologically active component of freshly crushed garlic), pyruvate and ammonia. The enzyme was crystallized in the presence of (+S)-allyl-L-cysteine, forming dendrite-like monoclinic crystals. In addition, intentionally produced apo-enzyme was crystallized in tetragonal form. These structures of alliinase with associated glycans were resolved to 1.4 A and 1.61 A by molecular replacement. Branched hexasaccharide chains N-linked to Asn146 and trisaccharide chains N-linked to Asn328 are seen. The structure of hexasaccharide was found similar to "short chain complex vacuole type" oligosaccharide most commonly seen in plant glycoproteins. An unexpected state of the enzyme active site has been observed in the present structure. The electron density in the region of the cofactor made it possible to identify the cofactor moiety as aminoacrylate intermediate covalently bound to the PLP cofactor. It was found in the present structure to be stabilized by large number of interactions with surrounding protein residues. Moreover, the existence of the expected internal aldimine bond between the epsilon-amino group of Lys251 and the aldehyde of the PLP is ruled out on the basis of a distinct separation of electron density of Lys251. The structure of the active site cavity in the apo-form is nearly identical to that seen in the holo-form, with two sulfate ions, an acetate and several water molecules from crystallization conditions that replace and mimic the PLP cofactor.

Two structures of alliinase from Alliium sativum L.: apo form and ternary complex with aminoacrylate reaction intermediate covalently bound to the PLP cofactor.,Shimon LJ, Rabinkov A, Shin I, Miron T, Mirelman D, Wilchek M, Frolow F J Mol Biol. 2007 Feb 16;366(2):611-25. Epub 2006 Nov 14. PMID:17174334^[1]

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

References

↑ Shimon LJ, Rabinkov A, Shin I, Miron T, Mirelman D, Wilchek M, Frolow F. Two structures of alliinase from Alliium sativum L.: apo form and ternary complex with aminoacrylate reaction intermediate covalently bound to the PLP cofactor. J Mol Biol. 2007 Feb 16;366(2):611-25. Epub 2006 Nov 14. PMID:17174334 doi:10.1016/j.jmb.2006.11.041

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/2hor"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2hor]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Allium_sativum Allium sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HOR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 1.6&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alliin_lyase Alliin lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.4 4.4.1.4] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2hor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hor OCA], [https://pdbe.org/2hor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hor RCSB], [https://www.ebi.ac.uk/pdbsum/2hor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hor ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/ALLN1_ALLSA ALLN1_ALLSA]] Able to cleave the C-S bond of sulfoxide derivatives of Cys to produce allicin, thus giving rise to all sulfur compounds which are responsible for most of the properties of garlic, such as the specific smell and flavor as well as the health benefits like blood lipid or blood pressure lowering.
+[https://www.uniprot.org/uniprot/ALLN1_ALLSA ALLN1_ALLSA] Able to cleave the C-S bond of sulfoxide derivatives of Cys to produce allicin, thus giving rise to all sulfur compounds which are responsible for most of the properties of garlic, such as the specific smell and flavor as well as the health benefits like blood lipid or blood pressure lowering.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ho/2hor_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>
   </jmolCheckbox>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Alliin lyase]]
 [[Category: Allium sativum]]
 [[Category: Large Structures]]
-[[Category: Frolow, F]]
+[[Category: Frolow F]]
-[[Category: Mirelman, D]]
+[[Category: Mirelman D]]
-[[Category: Rabinkov, A]]
+[[Category: Rabinkov A]]
-[[Category: Shimon, L J.W]]
+[[Category: Shimon LJW]]
-[[Category: Wilcheck, M]]
+[[Category: Wilcheck M]]
-[[Category: Alliinase]]
-[[Category: Aminoacrylate]]
-[[Category: Apo form]]
-[[Category: Garlic]]
-[[Category: Glycosylation]]
-[[Category: Lyase]]
-[[Category: Plant enzyme]]
-[[Category: Pyridoxal-5'-phosphate]]

2hor

From Proteopedia

Current revision

Crystal structure of alliinase from garlic- apo form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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