1XXX

Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis

Summary for 1XXX

• Entry DOI: 10.2210/pdb1xxx/pdb
• Descriptor: Dihydrodipicolinate synthase, MAGNESIUM ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: dihydrodipicolinate synthase, dapa, rv2753c, mycobacterium tuberculosis, lysine biosynthesis, structural genomics, psi, protein structure initiative, tb structural genomics consortium, tbsgc, lyase
• Biological source: Mycobacterium tuberculosis
• Cellular location: Cytoplasm (By similarity): P63945
• Total number of polymer chains: 8
• Total formula weight: 250635.89

Authors

Kefala, G.,Panjikar, S.,Janowski, R.,Weiss, M.S.,TB Structural Genomics Consortium (TBSGC) (deposition date: 2004-11-09, release date: 2006-02-14, Last modification date: 2024-10-30)

Primary citation

Kefala, G.,Evans, G.L.,Griffin, M.D.,Devenish, S.R.,Pearce, F.G.,Perugini, M.A.,Gerrard, J.A.,Weiss, M.S.,Dobson, R.C.
Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis.
Biochem.J., 411:351-360, 2008

PubMed Abstract: The three-dimensional structure of the enzyme dihydrodipicolinate synthase (KEGG entry Rv2753c, EC 4.2.1.52) from Mycobacterium tuberculosis (Mtb-DHDPS) was determined and refined at 2.28 A (1 A=0.1 nm) resolution. The asymmetric unit of the crystal contains two tetramers, each of which we propose to be the functional enzyme unit. This is supported by analytical ultracentrifugation studies, which show the enzyme to be tetrameric in solution. The structure of each subunit consists of an N-terminal (beta/alpha)(8)-barrel followed by a C-terminal alpha-helical domain. The active site comprises residues from two adjacent subunits, across an interface, and is located at the C-terminal side of the (beta/alpha)(8)-barrel domain. A comparison with the other known DHDPS structures shows that the overall architecture of the active site is largely conserved, albeit the proton relay motif comprising Tyr(143), Thr(54) and Tyr(117) appears to be disrupted. The kinetic parameters of the enzyme are reported: K(M)(ASA)=0.43+/-0.02 mM, K(M)(pyruvate)=0.17+/-0.01 mM and V(max)=4.42+/-0.08 micromol x s(-1) x mg(-1). Interestingly, the V(max) of Mtb-DHDPS is 6-fold higher than the corresponding value for Escherichia coli DHDPS, and the enzyme is insensitive to feedback inhibition by (S)-lysine. This can be explained by the three-dimensional structure, which shows that the (S)-lysine-binding site is not conserved in Mtb-DHDPS, when compared with DHDPS enzymes that are known to be inhibited by (S)-lysine. A selection of metabolites from the aspartate family of amino acids do not inhibit this enzyme. A comprehensive understanding of the structure and function of this important enzyme from the (S)-lysine biosynthesis pathway may provide the key for the design of new antibiotics to combat tuberculosis.

PubMed: 18062777
DOI: 10.1042/BJ20071360

Experimental method

X-RAY DIFFRACTION (2.28 Å)