ISDA: 1TWI

Deposition Date 2004-07-01

Release Date 2004-07-27

Last Version Date 2023-08-23

Entry Detail

PDB ID:

1TWI

Keywords:

LYASE

Title:

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine

Biological Source:

Source Organism:

Methanocaldococcus jannaschii (Taxon ID: 2190)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.20

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Diaminopimelate decarboxylase
Gene (Uniprot):lysA
Chain IDs:A, B, C, D
Chain Length:434
Number of Molecules:4
Biological Source:Methanocaldococcus jannaschii

UniProt ID:Q58497 Pfam ID:PF00278, PF02784

Ligand Molecules

LYS

PLP

Primary Citation

Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor

Rajashankar, K.R, Ray, S.S, Bonanno, J.B, Pinho, M.G, He, G, De Lencastre, H, Tomasz, A, Burley, S.K.Show

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.

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