Crystal Structure of Aspartate-Semialdehyde Dehydrogenase from Haemophilus influenzae

Experimental Data Snapshot

  • Resolution: 2.04 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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Capture of an Intermediate in the Catalytic Cycle of L-Aspartate-beta-Semialdehyde Dehydrogenase

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

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

  • DOI: https://doi.org/10.1073/pnas.1634958100
  • Primary Citation of Related Structures:  
    1NWC, 1NWH, 1NX6

  • PubMed 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.

  • Organizational Affiliation

    Department of Chemistry, University of Toledo, Toledo, OH 43606, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate-semialdehyde dehydrogenase
A, B
371Haemophilus influenzaeMutation(s): 0 
Gene Names: asd
Find proteins for P44801 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44801 
Go to UniProtKB:  P44801
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP44801
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.04 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.764α = 90
b = 109.878β = 90
c = 113.16γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Refinement description