3IC1

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Summary for 3IC1

• Entry DOI: 10.2210/pdb3ic1/pdb
• Descriptor: Succinyl-diaminopimelate desuccinylase, ZINC ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: dape, psi2, mcsg, zn bound, succinyl-diaminopimelate desuccinylase, structural genomics, protein structure initiative, midwest center for structural genomics, amino-acid biosynthesis, cobalt, diaminopimelate biosynthesis, hydrolase, lysine biosynthesis, metal-binding
• Biological source: Haemophilus influenzae
• Total number of polymer chains: 2
• Total formula weight: 83722.04

Authors

Nocek, B.P.,Gillner, D.M.,Holz, R.C.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2009-07-17, release date: 2009-09-22, Last modification date: 2023-09-06)

Primary citation

Nocek, B.P.,Gillner, D.M.,Fan, Y.,Holz, R.C.,Joachimiak, A.
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.
J.Mol.Biol., 397:617-626, 2010

PubMed Abstract: Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein, we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures, we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors.

PubMed: 20138056
DOI: 10.1016/j.jmb.2010.01.062

Experimental method

X-RAY DIFFRACTION (2.3 Å)