1PQU | pdb_00001pqu

Crystal Structure of the H277N Mutant of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae Bound with NADP, S-methyl cysteine sulfoxide and cacodylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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This is version 1.7 of the entry. See complete history


Literature

Critical catalytic functional groups in the mechanism of aspartate-beta-semialdehyde dehydrogenase.

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

(2004) Acta Crystallogr D Biol Crystallogr 60: 1808-1815

  • DOI: https://doi.org/10.1107/S0907444904020104
  • Primary Citation of Related Structures:  
    1PQP, 1PQU

  • PubMed Abstract: 

    Aspartate-beta-semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of beta-aspartyl phosphate to L-aspartate-beta-semialdehyde in the aspartate biosynthetic pathway. This pathway is not found in humans or other eukaryotic organisms, yet is required for the production of threonine, isoleucine, methionine and lysine in most microorganisms. The mechanism of this enzyme has been examined through the structures of two active-site mutants of ASADH from Haemophilus influenzae. Replacement of the enzyme active-site cysteine with serine (C136S) leads to a dramatic loss of catalytic activity caused by the expected decrease in nucleophilicity, but also by a change in the orientation of the serine hydroxyl group relative to the cysteine thiolate. In contrast, in the H277N active-site mutant the introduced amide is oriented in virtually the same position as that of the histidine imidazole ring. However, a shift in the position of the bound reaction intermediate to accommodate this shorter asparagine side chain, coupled with the inability of this introduced amide to serve as a proton acceptor, results in a 100-fold decrease in the catalytic efficiency of H277N relative to the native enzyme. These mutant enzymes have the same overall fold and high structural identity to native ASADH. However, small perturbations in the positioning of essential catalytic groups or reactive intermediates have dramatic effects on catalytic efficiency.


  • Organizational Affiliation
    • Department of Chemistry, University of Toledo, Toledo, Ohio 43606, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate-semialdehyde dehydrogenase
A, B, C, D
371Haemophilus influenzae Rd KW20Mutation(s): 1 
Gene Names: asd
EC: 1.2.1.11
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
N [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
CAC
Query on CAC

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
M [auth D]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CYS
Query on CYS

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
L [auth C],
O [auth D]
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.929α = 90
b = 76.579β = 92.59
c = 134.097γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-12-13
    Changes: Derived calculations
  • Version 1.6: 2024-11-20
    Changes: Structure summary
  • Version 1.7: 2025-11-12
    Changes: Database references