1P9L

Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 PDC

Summary for 1P9L

• Entry DOI: 10.2210/pdb1p9l/pdb
• Related: 1ARZ 1C3V 1DIH
• Descriptor: dihydrodipicolinate reductase, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, PYRIDINE-2,6-DICARBOXYLIC ACID, ... (5 entities in total)
• Functional Keywords: oxidoreductase, reductase, lysine biosynthesis, nadh binding specificity, tb structural genomics consortium, tbsgc, structural genomics, psi, protein structure initiative
• Biological source: Mycobacterium tuberculosis
• Cellular location: Cytoplasm (By similarity): P72024
• Total number of polymer chains: 2
• Total formula weight: 53446.11

Authors

Cirilli, M.,Zheng, R.,Scapin, G.,Blanchard, J.S.,TB Structural Genomics Consortium (TBSGC) (deposition date: 2003-05-12, release date: 2003-08-26, Last modification date: 2023-08-16)

Primary citation

Cirilli, M.,Zheng, R.,Scapin, G.,Blanchard, J.S.
The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity.
Biochemistry, 42:10644-10650, 2003

PubMed Abstract: Dihydrodipicolinate reductase (DHPR) catalyzes the reduced pyridine nucleotide-dependent reduction of the alpha,beta-unsaturated cyclic imine, dihydrodipicolinate, to generate tetrahydrodipicolinate. This enzyme catalyzes the second step in the bacterial biosynthetic pathway that generates meso-diaminopimelate, a component of bacterial cell walls, and the amino acid L-lysine. The Mycobacterium tuberculosis dapB-encoded DHPR has been cloned, expressed, purified, and crystallized in two ternary complexes with NADH or NADPH and the inhibitor 2,6-pyridinedicarboxylate (2,6-PDC). The structures have been solved using molecular replacement strategies, and the DHPR-NADH-2,6-PDC and DHPR-NADPH-2,6-PDC complexes have been refined against data to 2.3 and 2.5 A, respectively. The M. tuberculosis DHPR is a tetramer of identical subunits, with each subunit composed of two domains connected by two flexible hinge regions. The N-terminal domain binds pyridine nucleotide, while the C-terminal domain is involved in both tetramer formation and substrate/inhibitor binding. The M. tuberculosis DHPR uses NADH and NADPH with nearly equal efficiency based on V/K values. To probe the nature of this substrate specificity, we have generated two mutants, K9A and K11A, residues that are close to the 2'-phosphate of NADPH. These two mutants exhibit decreased specificity for NADPH by factors of 6- and 30-fold, respectively, but the K11A mutant exhibits 270% of WT activity using NADH. The highly conserved structure of the nucleotide fold may permit other enzyme's nucleotide specificity to be altered using similar mutagenic strategies.

PubMed: 12962488
DOI: 10.1021/bi030044v

Experimental method

X-RAY DIFFRACTION (2.3 Å)