3C0J

Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate

Summary for 3C0J

• Entry DOI: 10.2210/pdb3c0j/pdb
• Descriptor: Dihydrodipicolinate synthase, POTASSIUM ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: dihydrodipicolinate synthase, lysine biosynthase, amino-acid biosynthesis, diaminopimelate biosynthesis, lyase, lysine biosynthesis, schiff base
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A6L2
• Total number of polymer chains: 2
• Total formula weight: 63324.36

Authors

Dobson, R.C.J. (deposition date: 2008-01-21, release date: 2008-09-23, Last modification date: 2024-10-30)

Primary citation

Dobson, R.C.J.,Griffin, M.D.W.,Devenish, S.R.A.,Pearce, F.G.,Hutton, C.A.,Gerrard, J.A.,Jameson, G.B.,Perugini, M.A.
Conserved main-chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase
Protein Sci., 17:2080-2090, 2008

PubMed Abstract: In recent years, dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)-aspartate-beta-semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active-site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate analog, beta-hydroxypyruvate. The K (i) was determined to be 0.21 (+/-0.02) mM, similar to that of the allosteric inhibitor, (S)-lysine, and beta-hydroxypyruvate was observed to cause time-dependent inhibition. The inhibitory reaction with beta-hydroxypyruvate could be qualitatively followed by mass spectrometry, which showed initial noncovalent adduct formation, followed by the slow formation of the covalent adduct. It is unclear whether beta-hydroxypyruvate plays a role in regulating the biosynthesis of meso-diaminopimelate and (S)-lysine in E. coli, although we note that it is present in vivo. The crystal structure of DHDPS complexed with beta-hydroxypyruvate was solved. The active site clearly showed the presence of the inhibitor covalently bound to the Lys161. Interestingly, the hydroxyl group of beta-hydroxypyruvate was hydrogen-bonded to the main-chain carbonyl of Ile203. This provides insight into the possible catalytic role played by this peptide unit, which has a highly strained torsion angle (omega approximately 201 degrees ). A survey of the known DHDPS structures from other organisms shows this distortion to be a highly conserved feature of the DHDPS active site, and we propose that this peptide unit plays a critical role in catalysis.

PubMed: 18787203
DOI: 10.1110/ps.037440.108

Experimental method

X-RAY DIFFRACTION (2.4 Å)