1TUF image
Deposition Date 2004-06-24
Release Date 2004-07-20
Last Version Date 2024-04-03
Entry Detail
PDB ID:
1TUF
Keywords:
LYASE
Title:
Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi
Biological Source:
Source Organism:
Methanocaldococcus jannaschii (Taxon ID: 2190)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.40 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 61 2 2
1TUF validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Diaminopimelate decarboxylase
Gene (Uniprot):lysA
Chain IDs:A, B
Chain Length:434
Number of Molecules:2
Biological Source:Methanocaldococcus jannaschii
UniProt ID:Q58497 Pfam ID:PF02784, PF00278
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
LLP A LYS ?
Ligand Molecules
AZ1
Primary Citation
Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor
Structure 10 1499 1508 (2002)
PMID: 12429091 DOI: 10.1016/S0969-2126(02)00880-8

Abstact

Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1TUF