5J5D

Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with alpha-ketopimelic acid

Summary for 5J5D

• Entry DOI: 10.2210/pdb5j5d/pdb
• Descriptor: 4-hydroxy-tetrahydrodipicolinate synthase, SODIUM ION, 2-oxoheptanedioic acid, ... (4 entities in total)
• Functional Keywords: dap pathway, l-lysine, alpha-ketopimelic acid, lyase
• Biological source: Mycobacterium tuberculosis H37Rv
• Cellular location: Cytoplasm : P9WP25
• Total number of polymer chains: 1
• Total formula weight: 31108.35

Authors

Navratna, V.,Gopal, B. (deposition date: 2016-04-02, release date: 2016-08-17, Last modification date: 2023-11-08)

Primary citation

Shrivastava, P.,Navratna, V.,Silla, Y.,Dewangan, R.P.,Pramanik, A.,Chaudhary, S.,Rayasam, G.,Kumar, A.,Gopal, B.,Ramachandran, S.
Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues
Sci Rep, 6:30827-30827, 2016

PubMed Abstract: The Mycobacterium tuberculosis dihydrodipicolinate synthase (Mtb-dapA) is an essential gene. Mtb-DapA catalyzes the aldol condensation between pyruvate and L-aspartate-beta-semialdehyde (ASA) to yield dihydrodipicolinate. In this work we tested the inhibitory effects of structural analogues of pyruvate on recombinant Mtb-DapA (Mtb-rDapA) using a coupled assay with recombinant dihydrodipicolinate reductase (Mtb-rDapB). Alpha-ketopimelic acid (α-KPA) showed maximum inhibition of 88% and IC50 of 21 μM in the presence of pyruvate (500 μM) and ASA (400 μM). Competition experiments with pyruvate and ASA revealed competition of α-KPA with pyruvate. Liquid chromatography-mass spectrometry (LC-MS) data with multiple reaction monitoring (MRM) showed that the relative abundance peak of final product, 2,3,4,5-tetrahydrodipicolinate, was decreased by 50%. Thermal shift assays showed 1 °C Tm shift of Mtb-rDapA upon binding α-KPA. The 2.4 Å crystal structure of Mtb-rDapA-α-KPA complex showed the interaction of critical residues at the active site with α-KPA. Molecular dynamics simulations over 500 ns of pyruvate docked to Mtb-DapA and of α-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to α-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7 Å(2) are likely inhibitors. In summary, α-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA.

PubMed: 27501775
DOI: 10.1038/srep30827

Experimental method

X-RAY DIFFRACTION (2.4 Å)