PDBsum entry 2zy5

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Lyase PDB id
Protein chains
(+ 0 more) 510 a.a. *
PLP ×6
Waters ×1899
* Residue conservation analysis
PDB id:
Name: Lyase
Title: R487a mutant of l-aspartate beta-decarboxylase
Structure: L-aspartate beta-decarboxylase. Chain: a, b, c, d, e, f. Engineered: yes. Mutation: yes
Source: Alcaligenes faecalis subsp. Faecalis. Organism_taxid: 32001. Strain: subsp. Faecalis. Gene: asda-af. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.65Å     R-factor:   0.175     R-free:   0.238
Authors: H.-J.Chen,T.-P.Ko,C.-Y.Lee,N.-C.Wang,A.H.-J.Wang
Key ref:
H.J.Chen et al. (2009). Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase. Structure, 17, 517-529. PubMed id: 19368885 DOI: 10.1016/j.str.2009.02.013
13-Jan-09     Release date:   27-Jan-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q93QX0  (Q93QX0_ALCFA) -  Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase
533 a.a.
510 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: E.C.  - Aspartate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
+ 2-oxoglutarate
= oxaloacetate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
   Enzyme class 3: E.C.  - Aspartate 4-decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate = L-alanine + CO2
= L-alanine
+ CO(2)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   4 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1016/j.str.2009.02.013 Structure 17:517-529 (2009)
PubMed id: 19368885  
Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase.
H.J.Chen, T.P.Ko, C.Y.Lee, N.C.Wang, A.H.Wang.
The type-I PLP enzyme l-aspartate beta-decarboxylase converts aspartate to alanine and CO(2). Similar to the homodimeric aminotransferases, its protein subunit comprises a large and a small domain, of 410 and 120 residues, respectively. The crystal structure reveals a dodecamer made of six identical dimers arranged in a truncated tetrahedron whose assembly involves tetramer and hexamer as intermediates. The additional helical motifs I and II participate in the oligomer formation. Triple mutations of S67R/Y68R/M69R or S67E/Y68E/M69E in motif I produced an inactive dimer. The PLP is bound covalently to Lys315 in the active site, while its phosphate group interacts with a neighboring Tyr134. Removal of the bulky side chain of Arg37, which overhangs the PLP group, improved the substrate affinity. Mutations in flexible regions produced the more active K17A and the completely inactive R487A. The structure also suggests that substrate binding triggers conformational changes essential for catalyzing the reaction.
  Selected figure(s)  
Figure 4.
Figure 4. The pH Dependence of the Dodecamer Assembly of AsdA
(A) The distribution of molecular size under various pH conditions was assessed using AUC. Parameters used in calculating the sedimentation coefficients are viscosity = 0.01048 and density = 1.01029.
(B) The curve at pH 7.5 was converted to represent mass distribution. The corresponding masses of dimer and dodecamer were calculated using frictional coefficients f = 1.32–1.35, and those of the intermediates (inset; probably tetramer and hexamer) using f = 1.21–1.25.
(C) Areas under the curves in (A) were integrated to show different proportions of oligomers in various pH conditions. The ratio of dimer: intermediates: dodecamer was roughly 1:1:2 at pH 8.
(D) Under higher ionic strength of KCl, more dodecamers were dissociated into dimers at pH 7.
(E) The proposed assembly mechanism of ASD starts from monomer to dimer, followed by tetramer and two kinds of hexamer. Finally the two hexamers dock together, face to face, to form the spherical dodecamer.
Figure 5.
Figure 5. The Active Site Structure
(A) Stereoscopic view of the PLP binding site shows the surroundings of the bound cofactor (yellow). The phosphate group and the protonated nitrogen are salt-bridged to Arg323 and Asp286. The cyan Tyr134 is from another monomer.
(B) The active-site regions of two different subunits are superimposed. The L and S domains are colored cyan and green. N-terminal helix α1, and loops α6-α7 and βY-βZ, which contain Lys17, Tyr134, and Arg487, respectively, and the covering helix α9 are highlighted in purple, pink, red, and blue. Primed residue numbers are for the more open molecule.
(C) Surface presentation of the closed active site. Positive and negative charge potentials are indicated by blue and red colors. The loops and helices forming the active-site entrance are also shown.
(D) Surface of the more open active site. Intrinsic flexibility of domains, secondary structure elements, and loops should have caused the structural difference.
  The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 517-529) copyright 2009.  
  Figures were selected by an automated process.