Crystal structure of Aspartate semialdehyde dehydrogenase Complexed With inhibitor SMCS (CYS) And Phosphate From Mycobacterium tuberculosis H37Rv

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Structures of ternary complexes of aspartate-semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis H37Rv

Vyas, R.Tewari, R.Weiss, M.S.Karthikeyan, S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 671-679

  • DOI: https://doi.org/10.1107/S0907444912007330
  • Primary Citation of Related Structures:  
    3TZ6, 3VOS

  • PubMed Abstract: 

    Aspartate-semialdehyde dehydrogenase (Asd; ASADH; EC is the enzyme that lies at the first branch point in the biosynthetic pathway of important amino acids including lysine and methionine and the cell-wall component diaminopimelate (DAP). The enzymatic reaction of ASADH is the reductive dephosphorylation of aspartyl-β-phosphate (ABP) to aspartate β-semialdehyde (ASA). Since the aspartate pathway is absolutely essential for the survival of many microbes and is absent in humans, the enzymes involved in this pathway can be considered to be potential antibacterial drug targets. In this work, the structure of ASADH from Mycobacterium tuberculosis H37Rv (Mtb-ASADH) has been determined in complex with glycerol and sulfate at 2.18 Å resolution and in complex with S-methyl-L-cysteine sulfoxide (SMCS) and sulfate at 1.95 Å resolution. The overall structure of Mtb-ASADH is similar to those of its orthologues. However, in the Mtb-ASADH-glycerol complex structure the glycerol molecule is noncovalently bound to the active-site residue Cys130, while in the Mtb-ASADH-SMCS complex structure the SMCS (Cys) is covalently linked to Cys130. The Mtb-ASADH-SMCS complex structurally mimics one of the intermediate steps in the proposed mechanism of ASADH enzyme catalysis. Comparison of the two complex structures revealed that the amino acids Glu224 and Arg249 undergo conformational changes upon binding of glycerol. Moreover, the structures reported here may help in the development of species-specific antibacterial drug molecules against human pathogens.

  • Organizational Affiliation

    Department of Biotechnology, Panjab University, Chandigarh 160 014, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate-semialdehyde dehydrogenase344Mycobacterium tuberculosisMutation(s): 0 
Gene Names: asdMT3811MTV025.056cRv3708c
Find proteins for P9WNX5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNX5 
Go to UniProtKB:  P9WNX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNX5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CYS

Download Ideal Coordinates CCD File 
C3 H7 N O2 S
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 266.16α = 90
b = 266.16β = 90
c = 266.16γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description