PDBsum entry: 2qz9

Oxidoreductase

PDB id: 2qz9

Contents

Protein chains

336 a.a. *

Waters ×417

* Residue conservation analysis

PDB id:

2qz9

Name:

Oxidoreductase

Title:

Crystal structure of aspartate semialdehyde dehydrogenase ii from vibrio cholerae

Structure:

Aspartate-semialdehyde dehydrogenase. Chain: a, b, c. Synonym: asa dehydrogenase, asadh. Engineered: yes

Source:

Vibrio cholerae. Organism_taxid: 666. Strain: e1 tor n16961. Gene: asd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.201 R-free: 0.250

Authors:

R.E.Viola,X.Liu,J.F.Ohren,C.R.Faehnle

Key ref:

R.E.Viola et al. (2008). The structure of a redundant enzyme: a second isoform of aspartate beta-semialdehyde dehydrogenase in Vibrio cholerae. Acta Crystallogr D Biol Crystallogr, 64, 321-330. PubMed id: 18323627 DOI: 10.1107/S0907444907068552

Date:

16-Aug-07 Release date: 08-Apr-08

Protein chains

P23247  (DHAS_VIBCH) -  Aspartate-semialdehyde dehydrogenase 2

Seq: 337 a.a.

Struc: 336 a.a.

Enzyme reactions

• Enzyme class: E.C.1.2.1.11 - Aspartate-semialdehyde dehydrogenase.
• Pathway: Lysine biosynthesis (early stages)
• Reaction: L-aspartate 4-semialdehyde + phosphate + NADP⁺ = L-4-aspartyl phosphate + NADPH

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: oxidation-reduction process (9 terms)
• Biochemical function: nucleotide binding (8 terms)

reference

DOI no: 10.1107/S0907444907068552

Acta Crystallogr D Biol Crystallogr 64:321-330 (2008)

PubMed id: 18323627

The structure of a redundant enzyme: a second isoform of aspartate beta-semialdehyde dehydrogenase in Vibrio cholerae.

R.E.Viola, X.Liu, J.F.Ohren, C.R.Faehnle.

ABSTRACT

Aspartate-beta-semialdehyde dehydrogenase (ASADH) is an essential enzyme that is found in bacteria, fungi and plants but not in humans. ASADH produces the first branch-point metabolite in the biosynthetic pathways that lead to the production of lysine, threonine, methionine and isoleucine as well as the cell-wall precursor diaminopimelate. As a consequence, ASADH appears to be an excellent target for the development of novel antibiotics, especially for Gram-negative bacteria that require diaminopimelate for cell-wall biosynthesis. In contrast to the Gram-negative ASADHs, which readily formed well diffracting crystals, the second isoform of aspartate-beta-semialdehyde dehydrogenase from Vibrio cholerae (vcASADH2) was less well behaved in initial crystallization trials. In order to obtain good-quality single crystals of vcASADH2, a buffer-optimization protocol was used in which the initial purification buffer was exchanged into a new condition derived from a pre-crystalline hit. The unliganded structure of vcASADH2 has been determined to 2.2 A resolution to provide additional insight into the structural and functional evolution of the ASADH enzyme family. The overall fold and domain organization of this new structure is similar to the Gram-negative, Gram-positive and archeal ASADH structures determined previously, despite having less than 50% sequence identity to any of these family members. The substrate-complex structure reveals that the binding of L-aspartate-beta-semialdehyde (ASA) to vcASADH2 is accommodated by structural changes in the amino-acid binding site and in the helical subdomain that is involved in the dimer interface. Structural alignments show that this second isoform from Gram-negative V. cholerae most closely resembles the ASADH from a Gram-positive organism and is likely to bind the coenzyme in a different conformation to that observed in the other V. cholerae isoform.

Selected figure(s)

Figure 3.
Figure 3 Domain movement caused by ASA binding in vcASADH2. The binding of ASA to the active site induces a 5° rotation of the -helical dimerization subdomain towards the N-terminal domain. ASA, shown in stick representation, is covalently bound to Cys133. The fixed domain, the hinge-bending residues and the moved subdomain in the apo enzyme are colored blue, green and red, respectively. The complex structure is colored yellow and superimposed on the apo structure. The axis of domain movement is represented as a black dotted line.

Figure 7.
Figure 7 The NADP cofactor-binding sites in ASADHs. (a) There are significant differences in the NADP-binding pocket between the residues in vcASADH1 (white) and those in vcASADH2 (blue). (b) In contrast, the residues of spASADH (pink) align quite well with those of vcASADH2 (blue), suggesting a similar NADP-binding orientation. Dashed lines indicate the hydrogen bonds between NADP and binding residues within 3.5 Å.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 321-330) copyright 2008.

Figures were selected by an automated process.