1R0M

Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity

Summary for 1R0M

• Entry DOI: 10.2210/pdb1r0m/pdb
• Descriptor: N-acylamino acid racemase (2 entities in total)
• Functional Keywords: racemase, isomerase
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 4
• Total formula weight: 164242.66

Authors

Wang, W.-C.,Chiu, W.-C.,Hsu, S.-K.,Wu, C.-L.,Chen, C.-Y.,Liu, J.-S.,Hsu, W.-H. (deposition date: 2003-09-22, release date: 2004-09-22, Last modification date: 2024-03-13)

Primary citation

Wang, W.-C.,Chiu, W.-C.,Hsu, S.-K.,Wu, C.-L.,Chen, C.-Y.,Liu, J.-S.,Hsu, W.-H.
Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans
J.Mol.Biol., 342:155-169, 2004

PubMed 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.

PubMed: 15313614
DOI: 10.1016/j.jmb.2004.07.023

Experimental method

X-RAY DIFFRACTION (1.3 Å)