Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 97.47 kDa 
• Atom Count: 6946 
• Residue Count: 892 
• Unique protein chains: 1

1HKV

mycobacterium diaminopimelate dicarboxylase (lysa)

• DOI: 10.2210/pdb1HKV/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-03-11 Released: 2003-03-20 
• Deposition Author(s): Gokulan, K., Rupp, B., Pavelka Jr, M.S., Jacobs Jr, W.R., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

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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 

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

• PubMed: 12637582 
• DOI: 10.1074/jbc.M301549200
• Primary Citation of Related Structures:  
  1HKW, 1HKV


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIAMINOPIMELATE DECARBOXYLASE	A, B	453	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: lysA, Rv1293, MTCY373.13 EC: 4.1.1.20
Find proteins for P9WIU7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIU7  Go to UniProtKB:  P9WIU7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
LYS	A, B	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O

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 = 111.452	α = 90
b = 111.452	β = 90
c = 238.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-11 
• Released Date: 2003-03-20 
Deposition Author(s): Gokulan, K., Rupp, B., Pavelka Jr, M.S., Jacobs Jr, W.R., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Revision History 

• 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