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Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis

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Usha, Veeraraghavan, Dover, Lynn G., Roper, David I., Fuetterer, Klaus and Besra, Gurdyal S.. (2009) Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis. Acta Crystallographica Section D: Biological Crystallography, Vol.65 (No.4). pp. 383-387. ISSN 0907-4449

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Official URL: http://dx.doi.org/10.1107/S0907444909002522

Abstract

The meso (or d,L) isomer of diaminopimelic acid (DAP), a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan. While the peptidoglycan incorporated in the highly complex cell wall of the pathogen Mycobacterium tuberculosis structurally resembles that of Escherichia coli, it is unique in that it can contain penicillin-resistant meso-DAP -> meso-DAP linkages. The interconversion of L,L-DAP and meso-DAP is catalysed by the DAP epimerase DapF, a gene product that is essential in M. tuberculosis. Here, the crystal structure of the ligand-free form of M. tuberculosis DapF (MtDapF) refined to a resolution of 2.6 angstrom is reported. MtDapF shows small if distinct deviations in secondary structure from the two-domain alpha/beta-fold of the known structures of Haemophilus influenzae DapF and Bacillus anthracis DapF, which are in line with its low sequence identity (<= 27%) to the former. Modelling the present structure onto that of L,L-aziridino-DAP-bound H. influenzae DapF illustrates that a rigid-body movement of domain II and a rearrangement of the B4-A2 loop (residues 80-90) of domain I are likely to accompany the transition from the present inactive form to a catalytically competent enzyme. Despite a highly conserved active-site architecture, the model indicates that stabilization of the DAP backbone occurs in MtDapF through a tyrosine residue that is specific to mycobacterial DAP epimerases.

Item Type:

Journal Article

Subjects:

Q Science > QD Chemistry
Q Science > QH Natural history > QH301 Biology

Divisions:

Faculty of Science > Life Sciences (2010- ) > Biological Sciences ( -2010)

Journal or Publication Title:

Acta Crystallographica Section D: Biological Crystallography

Publisher:

Wiley-Blackwell Publishing, Inc.

ISSN:

0907-4449