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PDBsum entry 2hox

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Lyase PDB id
2hox
Jmol
Contents
Protein chains
425 a.a.
Ligands
NAG-FUC-NAG-BMA-
XYP-BMA
NAG ×8
P1T ×4
NAG-FUC
NAG-FUC-NAG-BMA
NAG-FUC-NAG
NAG-NAG
Metals
_CL ×4
Waters ×2669

References listed in PDB file
Key reference
Title Two structures of alliinase from alliium sativum l.: Apo form and ternary complex with aminoacrylate reaction intermediate covalently bound to the plp cofactor.
Authors L.J.Shimon, A.Rabinkov, I.Shin, T.Miron, D.Mirelman, M.Wilchek, F.Frolow.
Ref. J Mol Biol, 2007, 366, 611-625. [DOI no: 10.1016/j.jmb.2006.11.041]
PubMed id 17174334
Abstract
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.
Figure 2.
Figure 2. (a) Stereo plot of the final |2F[o]–F[c]| electron density maps contoured at 1σ, in the immediate vicinity of the PLP-AA molecule and the surrounding protein region. The molecules are colored by atom type. The position of Lys251 is labeled. Prepared with BOBSCRIPT.^71^,^72 (b) The catalytic pocket and the PLP-AA intermediate. Hydrogen bonds to the interacting residues of the protein and to the relevant water molecules are shown as blue dotted lines. Figure 2. (a) Stereo plot of the final |2F[o]–F[c]| electron density maps contoured at 1σ, in the immediate vicinity of the PLP-AA molecule and the surrounding protein region. The molecules are colored by atom type. The position of Lys251 is labeled. Prepared with BOBSCRIPT.[3]^71^,[4]^72 (b) The catalytic pocket and the PLP-AA intermediate. Hydrogen bonds to the interacting residues of the protein and to the relevant water molecules are shown as blue dotted lines. Prepared with MOLSCRIPT.[5]^73
Figure 5.
Figure 5. Superposition of the alliinase active site residues. The PLP-AA external aldimine form is in gray and the active site of PLP-AA C-S lyase (1ELU) is in cyan. In both cases the cofactor ring tilts away from the catalytic lysine residue. The guanadinium groups of residues Arg401 and Arg369 make equivalent hydrogen bonding interactions with either the aminoacrylate moiety of the PLP-AA. Figure 5. Superposition of the alliinase active site residues. The PLP-AA external aldimine form is in gray and the active site of PLP-AA C-S lyase (1ELU) is in cyan. In both cases the cofactor ring tilts away from the catalytic lysine residue. The guanadinium groups of residues Arg401 and Arg369 make equivalent hydrogen bonding interactions with either the aminoacrylate moiety of the PLP-AA.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 366, 611-625) copyright 2007.
Secondary reference #1
Title Alliin lyase (alliinase) from garlic (allium sativum): crystallization and preliminary X-Ray characterization.
Authors L.J.Shimon, A.Rabinkov, T.Miron, D.Mirelman, M.Wilchek, F.Frolow.
Ref. Acta Crystallogr D Biol Crystallogr, 2002, 58, 1335-1337. [DOI no: 10.1107/S0907444902010466]
PubMed id 12136147
Full text Abstract
Figure 1.
Figure 1 The reaction catalyzed by aliinase.
Figure 3.
Figure 3 Crystal of A. sativum alliinase. The largest dimension is 0.1 mm.
The above figures are reproduced from the cited reference with permission from the IUCr
PROCHECK
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