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PDBsum entry 1lk9

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1lk9
Jmol
Contents
Protein chains
425 a.a. *
Ligands
NAG-FUC-NAG-BMA
NAG-NAG ×2
SO4 ×11
PLP
EPE ×2
NAG-FUC
PLP-DHA
Metals
_CL ×2
Waters ×830
* Residue conservation analysis
PDB id:
1lk9
Name: Lyase
Title: The three-dimensional structure of alliinase from garlic
Structure: Alliin lyase. Chain: a, b. Synonym: alliinase, cysteine sulphoxide lyase. Ec: 4.4.1.4
Source: Allium sativum. Garlic. Organism_taxid: 4682. Other_details: bulb
Biol. unit: Dimer (from PQS)
Resolution:
1.53Å     R-factor:   0.193     R-free:   0.221
Authors: E.B.Kuettner,R.Hilgenfeld,M.S.Weiss
Key ref:
E.B.Kuettner et al. (2002). The active principle of garlic at atomic resolution. J Biol Chem, 277, 46402-46407. PubMed id: 12235163 DOI: 10.1074/jbc.M208669200
Date:
24-Apr-02     Release date:   11-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
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 = DHA)
corresponds exactly
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% 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: 10.1074/jbc.M208669200 J Biol Chem 277:46402-46407 (2002)
PubMed id: 12235163  
 
 
The active principle of garlic at atomic resolution.
E.B.Kuettner, R.Hilgenfeld, M.S.Weiss.
 
  ABSTRACT  
 
Despite the fact that many cultures around the world value and utilize garlic as a fundamental component of their cuisine as well as of their medicine cabinets, relatively little is known about the plant's protein configuration that is responsible for the specific properties of garlic. Here, we report the three-dimensional structure of the garlic enzyme alliinase at 1.5 A resolution. Alliinase constitutes the major protein component in garlic bulbs, and it is able to cleave carbon-sulfur bonds. The active enzyme is a pyridoxal-5'-phosphate-dependent homodimeric glycoprotein and belongs to the class I family of pyridoxal-5'-phosphate-dependent enzymes. In addition, it contains a novel epidermal growth factor-like domain that makes it unique among all pyridoxal-5'-phosphate-dependent enzymes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. A, therapeutically active sulfur compounds from garlic; a representative for each of the three substance classes (allyl sulfides, dithiines, and ajoenes) is shown. B, the enzymatic reaction catalyzed by alliinase.
Figure 6.
Fig. 6. The active site of alliinase from garlic. A, stereo diagram of all residues in hydrogen bonding distance to either the cofactor PLP ( yellow) or the modeled substrate alliin. B, schematic diagram of the active site architecture. Both alliin configurations are shown: (+)-alliin, (magenta) and ( )-alliin, (cyan). Hydrogen bonding distances are given in Å.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 46402-46407) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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.  
  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.  
18394996 Y.Tao, J.L.Ferrer, K.Ljung, F.Pojer, F.Hong, J.A.Long, L.Li, J.E.Moreno, M.E.Bowman, L.J.Ivans, Y.Cheng, J.Lim, Y.Zhao, C.L.Ballaré, G.Sandberg, J.P.Noel, and J.Chory (2008).
Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants.
  Cell, 133, 164-176.
PDB code: 3bwn
17327674 C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, and M.S.Weiss (2007).
On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
  Acta Crystallogr D Biol Crystallogr, 63, 366-380.
PDB codes: 2g4h 2g4i 2g4j 2g4k 2g4l 2g4m 2g4n 2g4o 2g4p 2g4q 2g4r 2g4s 2g4t 2g4u 2g4v 2g4w 2g4x 2g4y 2g4z 2g51 2g52 2g55 2ill
16131760 C.Mueller-Dieckmann, S.Panjikar, P.A.Tucker, and M.S.Weiss (2005).
On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.
  Acta Crystallogr D Biol Crystallogr, 61, 1263-1272.
PDB codes: 2a7a 2a7b 2a7c 2a7d 2a7e 2a7f 2a7g 2a7h 2a7i 2a7j
15968116 K.Djinović Carugo, J.R.Helliwell, H.Stuhrmann, and M.S.Weiss (2005).
Softer and soft X-rays in macromolecular crystallography.
  J Synchrotron Radiat, 12, 410-419.  
15772310 M.A.Wouters, I.Rigoutsos, C.K.Chu, L.L.Feng, D.B.Sparrow, and S.L.Dunwoodie (2005).
Evolution of distinct EGF domains with specific functions.
  Protein Sci, 14, 1091-1103.  
16010345 P.Rose, M.Whiteman, P.K.Moore, and Y.Z.Zhu (2005).
Bioactive S-alk(en)yl cysteine sulfoxide metabolites in the genus Allium: the chemistry of potential therapeutic agents.
  Nat Prod Rep, 22, 351-368.  
15965542 R.Bentley (2005).
Role of sulfur chirality in the chemical processes of biology.
  Chem Soc Rev, 34, 609-624.  
15498941 A.Paiardini, F.Bossa, and S.Pascarella (2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
  Protein Sci, 13, 2992-3005.  
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 code is shown on the right.