PDBsum entry 1xpy

Isomerase

PDB id: 1xpy

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

Protein chains

Q9RYA6  (Q9RYA6_DEIRA) -  N-succinylamino acid racemase from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 375 a.a.

Struc: 360 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.2.1.113 - o-succinylbenzoate synthase.
• Reaction: (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O
• Cofactor: Mn(2+) or Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

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.