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PDBsum entry 2hor

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protein ligands metals links
Lyase PDB id
2hor
Jmol
Contents
Protein chain
425 a.a. *
Ligands
NAG-FUC-NAG-BMA-
MAN-MAN
NAG
SO4 ×5
ACT
NO3
Metals
_CL ×2
Waters ×496
* Residue conservation analysis
PDB id:
2hor
Name: Lyase
Title: Crystal structure of alliinase from garlic- apo form
Structure: Alliin lyase 1. Chain: a. Fragment: alliine lyase 1. Synonym: alliinase 1, cysteine sulphoxide lyase 1. Ec: 4.4.1.4
Source: Allium sativum. Garlic. Organism_taxid: 4682
Resolution:
1.60Å     R-factor:   0.164     R-free:   0.179
Authors: L.J.W Shimon,A.Rabinkov,M.Wilcheck,D.Mirelman,F.Frolow
Key ref:
L.J.Shimon et al. (2007). 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, 366, 611-625. PubMed id: 17174334 DOI: 10.1016/j.jmb.2006.11.041
Date:
16-Jul-06     Release date:   06-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q01594  (ALLN1_ALLSA) -  Alliin lyase 1
Seq:
Struc:
486 a.a.
425 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.4.1.4  - Alliin lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An S-alkyl-L-cysteine S-oxide = an alkyl sulfenate + 2-aminoacrylate
S-alkyl-L-cysteine S-oxide
= alkyl sulfenate
+
2-aminoacrylate
Bound ligand (Het Group name = ACT)
matches with 66.67% similarity
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = NAG) matches with 50.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     vacuole   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.11.041 J Mol Biol 366:611-625 (2007)
PubMed id: 17174334  
 
 
Two Structures of Alliinase from Alliium sativum L.: Apo Form and Ternary Complex with Aminoacrylate Reaction Intermediate Covalently Bound to the PLP Cofactor.
L.J.Shimon, A.Rabinkov, I.Shin, T.Miron, D.Mirelman, M.Wilchek, F.Frolow.
 
  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.
 
  Selected figure(s)  
 
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.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20678009 E.Appel, A.Rabinkov, M.Neeman, F.Kohen, and D.Mirelman (2011).
Conjugates of daidzein-alliinase as a targeted pro-drug enzyme system against ovarian carcinoma.
  J Drug Target, 19, 326-335.  
  21255165 Z.Y.Zhou, C.G.Zhang, L.Wu, C.G.Zhang, J.Chai, M.Wang, A.Jha, P.F.Jia, S.J.Cui, M.Yang, R.Chen, and G.Q.Guo (2011).
Functional characterization of the CKRC1/TAA1 gene and dissection of hormonal actions in the Arabidopsis root.
  Plant J, 66, 516-527.  
19949059 E.Appel, A.Vallon-Eberhard, A.Rabinkov, O.Brenner, I.Shin, K.Sasson, Y.Shadkchan, N.Osherov, S.Jung, and D.Mirelman (2010).
Therapy of murine pulmonary aspergillosis with antibody-alliinase conjugates and alliin.
  Antimicrob Agents Chemother, 54, 898-906.  
20370823 K.Nishio, K.Ogasahara, Y.Morimoto, T.Tsukihara, S.J.Lee, and K.Yutani (2010).
Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.
  FEBS J, 277, 2157-2170.
PDB codes: 2dh5 2dh6
21081698 M.Koutmos, O.Kabil, J.L.Smith, and R.Banerjee (2010).
Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine {beta}-synthase.
  Proc Natl Acad Sci U S A, 107, 20958-20963.
PDB codes: 3pc2 3pc3 3pc4
  19177363 L.Weiner, I.Shin, L.J.Shimon, T.Miron, M.Wilchek, D.Mirelman, F.Frolow, and A.Rabinkov (2009).
Thiol-disulfide organization in alliin lyase (alliinase) from garlic (Allium sativum).
  Protein Sci, 18, 196-205.  
18346080 C.Jacob, and A.Anwar (2008).
The chemistry behind redox regulation with a focus on sulphur redox systems.
  Physiol Plant, 133, 469-480.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.