1HKV

mycobacterium diaminopimelate dicarboxylase (lysa)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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Literature

Crystal Structure of Mycobacterium Tuberculosis Diaminopimelate Decarboxylase, an Essential Enzyme in Bacterial Lysine Biosynthesis

Gokulan, K., Rupp, B., Pavelka, M., Jacobs, W., Sacchettini, J.C.

(2003) J Biol Chem 278: 18588

  • DOI: 10.1074/jbc.M301549200
  • Primary Citation of Related Structures:  
    1HKV, 1HKW

  • PubMed Abstract: 

    • The Mycobacterium tuberculosis lysA gene encodes the enzyme meso-diaminopimelate decarboxylase (DAPDC), a pyridoxal-5'-phosphate (PLP)-dependent enzyme. The enzyme catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine ...

    The Mycobacterium tuberculosis lysA gene encodes the enzyme meso-diaminopimelate decarboxylase (DAPDC), a pyridoxal-5'-phosphate (PLP)-dependent enzyme. The enzyme catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. The lysA gene of M. tuberculosis H37Rv has been established as essential for bacterial survival in immunocompromised mice, demonstrating that de novo biosynthesis of lysine is essential for in vivo viability. Drugs targeted against DAPDC could be efficient anti-tuberculosis drugs, and the three-dimensional structure of DAPDC from M. tuberculosis complexed with reaction product lysine and the ternary complex with PLP and lysine in the active site has been determined. The first structure of a DAPDC confirms its classification as a fold type III PLP-dependent enzyme. The structure shows a stable 2-fold dimer in head-to-tail arrangement of a triose-phosphate isomerase (TIM) barrel-like alpha/beta domain and a C-terminal beta sheet domain, similar to the ornithine decarboxylase (ODC) fold family. PLP is covalently bound via an internal aldimine, and residues from both domains and both subunits contribute to the binding pocket. Comparison of the structure with eukaryotic ODCs, in particular with a di-fluoromethyl ornithine (DMFO)-bound ODC from Trypanosoma bruceii, indicates that corresponding DAP-analogues might be potential inhibitors for mycobacterial DAPDCs.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIAMINOPIMELATE DECARBOXYLASEA, B453Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: lysA, Rv1293, MTCY373.13
EC: 4.1.1.20
UniProt
Find proteins for P9WIU7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIU7 
Go to UniProtKB:  P9WIU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WIU7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
LYS
Query on LYS
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.452α = 90
b = 111.452β = 90
c = 238.253γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-20
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Structure summary
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.3: 2019-08-21
    Changes: Data collection, Database references