PDBsum entry: 1nx6

Oxidoreductase

PDB-id: 1nx6

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

357 a.a. *

Ligands

PO4 ×2

Waters ×144

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, dimer
(*as deduced by PQS)

PDB id:

1nx6

Name:

Oxidoreductase

Title:

Crystal structure of aspartate semialdehyde dehydrogenase from haemophilus influenzae as a tetrahedral hemithiocetal reaction intermediate with phosphate at 2.15 a

Structure:

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

Source:

Haemophilus influenzae. Organism_taxid: 727. Gene: asd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biological unit:

Dimer (from PQS)

UniProt:

P44801 (DHAS_HAEIN)

Seq:

Struc:

Seq:

371 a.a.

Struc:

357 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme class:

E.C.1.2.1.11   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

L-aspartate 4-semialdehyde + phosphate + NADP⁺ = L-4-aspartyl phosphate + NADPH (see diagram below)

Pathway:

Lysine biosynthesis (early stages)

Resolution:

2.15Å

R-factor:

0.228

R-free:

0.284

Authors:

J.Blanco,R.A.Moore,R.E.Viola

Key ref:

J.Blanco et al. (2003). Capture of an intermediate in the catalytic cycle of L-aspartate-beta-semialdehyde dehydrogenase.. Proc Natl Acad Sci U S A, 100, 12613-12617. [PubMed id: 14559965] [DOI: 10.1073/pnas.1634958100]

Date:

09-Feb-03

Release date:

04-Nov-03

Related entries:

1mb4
aspartate semialdehyde dehydrogenase from vibrio cholerae
with NADP and s-methyl-l-cysteine sulfoxide
1mc4
aspartate semialdehyde from vibrio cholerae
1gl3
aspartate beta-semialdehyde dehydrogenase in complex with
NADP and substrate analogue s-methyl cysteine sulfoxide
1brm
aspartate beta-semialdehyde dehydrogenase from escherichia
... plus others (see Header records)

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Clefts

Surface

Key reference

DOI no: 10.1073/pnas.1634958100

Proc Natl Acad Sci U S A 100:12613-12617 (2003)

PubMed id: 14559965

Capture of an intermediate in the catalytic cycle of L-aspartate-beta-semialdehyde dehydrogenase.

J.Blanco, R.A.Moore, R.E.Viola.

ABSTRACT

The structural analysis of an enzymatic reaction intermediate affords a unique opportunity to study a catalytic mechanism in extraordinary detail. Here we present the structure of a tetrahedral intermediate in the catalytic cycle of aspartate-beta-semialdehyde dehydrogenase (ASADH) from Haemophilus influenzae at 2.0-A resolution. ASADH is not found in humans, yet its catalytic activity is required for the biosynthesis of essential amino acids in plants and microorganisms. Diaminopimelic acid, also formed by this enzymatic pathway, is an integral component of bacterial cell walls, thus making ASADH an attractive target for the development of new antibiotics. This enzyme is able to capture the substrates aspartate-beta-semialdehyde and phosphate as an active complex that does not complete the catalytic cycle in the absence of NADP. A distinctive binding pocket in which the hemithioacetal oxygen of the bound substrate is stabilized by interaction with a backbone amide group dictates the R stereochemistry of the tetrahedral intermediate. This pocket, reminiscent of the oxyanion hole found in serine proteases, is completed through hydrogen bonding to the bound phosphate substrate.

Selected figure(s)

Figure 4.
Fig. 4. Schematic representation of the ASADH active site with a bound hemithioacetal reaction intermediate. Interactions between ASA and phosphate and key active site residues are shown.

Figure 6.
Fig. 6. Proposed mechanism for the catalytic cycle of ASADH shown in reverse biological direction. (A) Tetrahedral intermediate derived from reaction with ASA. (B) Proposed acyl intermediate with trigonal planar geometry. (C) Second tetrahedral intermediate with covalently bound aspartyl phosphate.

Figures were selected by an automated process.