PDBsum entry 2ggj

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Isomerase PDB id
Jmol PyMol
Protein chains
360 a.a. *
Waters ×761
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: The mutant y218c of deinococcus radiodurans n-acylamino acid racemase
Structure: N-acylamino acid racemase. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Deinococcus radiodurans. Organism_taxid: 1299. Strain: ccrc 12827. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
2.50Å     R-factor:   0.164     R-free:   0.208
Authors: W.C.Wang,W.C.Chiu
Key ref:
W.C.Chiu et al. (2006). Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J Mol Biol, 359, 741-753. PubMed id: 16650857 DOI: 10.1016/j.jmb.2006.03.063
24-Mar-06     Release date:   11-Apr-06    
Supersedes: 2fkt
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9RYA6  (Q9RYA6_DEIRA) -  o-succinylbenzoate synthase
375 a.a.
360 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Amino-acid racemase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An L-amino acid = a D-amino acid
L-amino acid
= D-amino acid
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     menaquinone biosynthetic process   1 term 
  Biochemical function     lyase activity     4 terms  


DOI no: 10.1016/j.jmb.2006.03.063 J Mol Biol 359:741-753 (2006)
PubMed id: 16650857  
Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase.
W.C.Chiu, J.Y.You, J.S.Liu, S.K.Hsu, W.H.Hsu, C.H.Shih, J.K.Hwang, W.C.Wang.
N-Acylamino acid racemase (NAAAR) and N-carbamoyl-D-amino-acid amidohydrolase (D-NCAase) are important biocatalysts for producing enantiopure alpha-amino acids. NAAAR forms an octameric assembly and displays induced fit movements upon substrate binding, while D-NCAase is a tetramer that does not change conformation in the presence of a ligand. To investigate the effects of introducing potentially stabilizing S-S bridges in these different multimeric enzymes, cysteine residues predicted to form inter or intra-subunit disulfide bonds were introduced by site-directed mutagenesis. Inter-subunit S-S bonds were formed in two NAAAR variants (A68C-D72C and P60C-Y100C) and two d-NCAase variants (A302C and P295C-F304C). Intra-subunit S-S bonds were formed in two additional NAAAR variants (E149C-A182C and V265C). Crystal structures of NAAARs variants show limited deviations from the wild-type overall tertiary structure. An apo A68C-D72C subunit differs from the wild-type enzyme, in which it has an ordered lid loop, resembling ligand-bound NAAAR. The structures of A222C and A302C D-NCAases are nearly identical to the wild-type enzyme. All mutants with inter-subunit bridges had increases in thermostability. Compared with the wild-type enzyme, A68C-D72C NAAAR showed similar kcat/Km ratios, whereas mutant D-NCAases demonstrated increased kcat/Km ratios at high temperatures (A302C: 4.2-fold at 65 degrees C). Furthermore, molecular dynamic simulations reveal that A302C substantially sustains the fine-tuned catalytic site as temperature increases, achieving enhanced activity.
  Selected figure(s)  
Figure 2.
Figure 2. (a) Ribbon representation of the octameric A68C-D72C NAAAR structure viewed down the 4-fold axis. (b) Stereo representation of the monomeric A68C-D72C NAAAR structure. (c) Stereo representation of the disulfide bonds at the interface between each A–C dimer of A68C-D72C are depicted as ball-and-stick models, in which the oxygen, nitrogen and sulfur atoms are in red, blue, and yellow, respectively. The 2F[o]−F[c] map is contoured at the 1.0σ level.
Figure 3.
Figure 3. (a) Superimposed C subunits of A68C-D72C·Mg^2+·NAQ and NAAAR·Mg^2+·NAQ. The C^α traces of the wild-type NAAAR and A68C-D72C are shown in yellow and green, respectively. (b) Stereo representation of NAQ shown as ball-and-stick models. The oxygen, nitrogen and Mg atoms are in red, blue, and green, respectively. The F[o]−F[c] maps of NAQ and Mg^2+ are contoured at the 1.0σ level.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 741-753) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21360152 D.Zhang, F.Zhu, W.Fan, R.Tao, H.Yu, Y.Yang, W.Jiang, and S.Yang (2011).
Gradually accumulating beneficial mutations to improve the thermostability of N-carbamoyl-D-amino acid amidohydrolase by step-wise evolution.
  Appl Microbiol Biotechnol, 90, 1361-1371.  
21210121 S.C.Kan, L.K.Yu, J.H.Chen, H.Y.Hu, and W.H.Hsu (2011).
Mutational analysis of splicing activities of ribonucleotide reductase α subunit protein from lytic bacteriophage P1201.
  Curr Microbiol, 62, 1282-1286.  
18985337 H.Yu, J.Li, D.Zhang, Y.Yang, W.Jiang, and S.Yang (2009).
Improving the thermostability of N-carbamyl-D-amino acid amidohydrolase by error-prone PCR.
  Appl Microbiol Biotechnol, 82, 279-285.  
18214979 M.Hayashida, S.H.Kim, K.Takeda, T.Hisano, and K.Miki (2008).
Crystal structure of N-acylamino acid racemase from Thermus thermophilus HB8.
  Proteins, 71, 519-523.
PDB code: 2zc8
17307742 C.L.Hung, J.H.Liu, W.C.Chiu, S.W.Huang, J.K.Hwang, and W.C.Wang (2007).
Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad.
  J Biol Chem, 282, 12220-12229.
PDB codes: 2dyu 2dyv 2e2k 2e2l
17416655 D.Vidal-Ingigliardi, S.Lewenza, and N.Buddelmeijer (2007).
Identification of essential residues in apolipoprotein N-acyl transferase, a member of the CN hydrolase family.
  J Bacteriol, 189, 4456-4464.  
17075931 M.T.Reetz, J.D.Carballeira, and A.Vogel (2006).
Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability.
  Angew Chem Int Ed Engl, 45, 7745-7751.  
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