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PDBsum entry 1xpy

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
1xpy
Jmol
Contents
Protein chains
360 a.a. *
Ligands
NLQ ×2
Metals
_MG ×4
Waters ×842
* Residue conservation analysis
PDB id:
1xpy
Name: Isomerase
Title: Structural basis for catalytic racemization and substrate specificity of an n-acylamino acid racemase homologue from deinococcus radiodurans
Structure: N-acylamino acid racemase. Chain: a, b, c, d. Engineered: yes
Source: Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.30Å     R-factor:   0.174     R-free:   0.227
Authors: W.-C.Wang,W.-C.Chiu,S.-K.Hsu,C.-L.Wu,C.-Y.Chen,J.-S.Liu,W.- H.Hsu
Key ref:
W.C.Wang et al. (2004). Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans. J Mol Biol, 342, 155-169. PubMed id: 15313614 DOI: 10.1016/j.jmb.2004.07.023
Date:
10-Oct-04     Release date:   26-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9RYA6  (Q9RYA6_DEIRA) -  N-acylamino acid racemase
Seq:
Struc:
375 a.a.
360 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1016/j.jmb.2004.07.023 J Mol Biol 342:155-169 (2004)
PubMed id: 15313614  
 
 
Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans.
W.C.Wang, W.C.Chiu, S.K.Hsu, C.L.Wu, C.Y.Chen, J.S.Liu, W.H.Hsu.
 
  ABSTRACT  
 
N-acylamino acid racemase (NAAAR) catalyzes the racemization of N-acylamino acids and can be used in concert with an aminoacylase to produce enantiopure alpha-amino acids, a process that has potential industrial applications. Here we have cloned and characterized an NAAAR homologue from a radiation-resistant ancient bacterium, Deinococcus radiodurans. The expressed NAAAR racemized various substrates at an optimal temperature of 60 degrees C and had Km values of 24.8 mM and 12.3 mM for N-acetyl-D-methionine and N-acetyl-L-methionine, respectively. The crystal structure of NAAAR was solved to 1.3 A resolution using multiwavelength anomalous dispersion (MAD) methods. The structure consists of a homooctamer in which each subunit has an architecture characteristic of enolases with a capping domain and a (beta/alpha)7 beta barrel domain. The NAAAR.Mg2+ and NAAAR.N-acetyl-L-glutamine.Mg2+ structures were also determined, allowing us to define the Lys170-Asp195-Glu220-Asp245-Lys269 framework for catalyzing 1,1-proton exchange of N-acylamino acids. Four subsites enclosing the substrate are identified: catalytic site, metal-binding site, side-chain-binding region, and a flexible lid region. The high conservation of catalytic and metal-binding sites in different enolases reflects the essentiality of a common catalytic platform, allowing these enzymes to robustly abstract alpha-protons of various carboxylate substrates efficiently. The other subsites involved in substrate recognition are less conserved, suggesting that divergent evolution has led to functionally distinct enzymes.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The binding pocket in the NAAAR·NAQ·Mg2+ ternary complex. (a) Stereoview of the active site of the NAAAR·NAQ·Mg2+ complex. NAQ (dark green) is shown as a ball-and-stick model with carbon atoms colored white. Five loops enclosing NAQ are green. Residues in C sub-site (red), M sub-site (blue), S sub-site (purple), and L region (yellow) are shown as stick models. The oxygen and nitrogen atoms are red and blue, respectively. The magnesium ion is shown in green. (b) Schematic representation of interactions between NAQ and NAAAR. The color representation of the four sub-sites is as in (a). The hydrogen-bonding interactions are shown as broken lines.
Figure 8.
Figure 8. Comparison of binding pockets in enolases. (a) Superposition of binding pockets in the apo structures of NAAAR (green), MLE (brown), YkfB (pink), and YcjG (cyan). The S and L regions are shown as C^a traces and conserved carboxylate residues and two catalytic Lys residues corresponding to Lys170, Asp195, Glu220, Asp245, and Lys269 in NAAAR are shown as stick models. The oxygen, nitrogen, and sulfur atoms are red, blue, and yellow, respectively. (b) The binding pockets of NAAAR (green), MAL (cyan), enolase (brown), and MR (pink) were superimposed. The S and L (L1 and L2) sites are shown as C^a traces and conserved carboxylate residues and catalytic residues corresponding to Lys170, Asp195, Glu220, Asp245, and Lys269 in NAAAR are shown as stick models. The bound ligand is shown as thin sticks.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 155-169) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19502445 I.C.Chen, W.D.Lin, S.K.Hsu, V.Thiruvengadam, and W.H.Hsu (2009).
Isolation and characterization of a novel lysine racemase from a soil metagenomic library.
  Appl Environ Microbiol, 75, 5161-5166.  
19517534 J.Pozo-Dengra, S.Martínez-Rodríguez, L.M.Contreras, J.Prieto, M.Andújar-Sánchez, J.M.Clemente-Jiménez, F.J.Las Heras-Vázquez, F.Rodríguez-Vico, and J.L.Neira (2009).
Structure and conformational stability of a tetrameric thermostable N-succinylamino acid racemase.
  Biopolymers, 91, 757-772.  
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
17137304 S.K.Hsu, H.H.Lo, C.H.Kao, D.S.Lee, and W.H.Hsu (2006).
Enantioselective synthesis of L-homophenylalanine by whole cells of recombinant Escherichia coli expressing L-aminoacylase and N-acylamino acid racemase genes from Deinococcus radiodurans BCRC12827.
  Biotechnol Prog, 22, 1578-1584.  
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.