Tags

Type your tag names separated by a space and hit enter

Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia.
J Mol Biol. 2007 Aug 17; 371(3):685-702.JM

Abstract

The essential biosynthetic pathway to l-Lysine in bacteria and plants is an attractive target for the development of new antibiotics or herbicides because it is absent in humans, who must acquire this amino acid in their diet. Plants use a shortcut of a bacterial pathway to l-Lysine in which the pyridoxal-5'-phosphate (PLP)-dependent enzyme ll-diaminopimelate aminotransferase (LL-DAP-AT) transforms l-tetrahydrodipicolinic acid (L-THDP) directly to LL-DAP. In addition, LL-DAP-AT was recently found in Chlamydia sp., suggesting that inhibitors of this enzyme may also be effective against such organisms. In order to understand the mechanism of this enzyme and to assist in the design of inhibitors, the three-dimensional crystal structure of LL-DAP-AT was determined at 1.95 A resolution. The cDNA sequence of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) was optimized for expression in bacteria and cloned in Escherichia coli without its leader sequence but with a C-terminal hexahistidine affinity tag to aid protein purification. The structure of AtDAP-AT was determined using the multiple-wavelength anomalous dispersion (MAD) method with a seleno-methionine derivative. AtDAP-AT is active as a homodimer with each subunit having PLP in the active site. It belongs to the family of type I fold PLP-dependent enzymes. Comparison of the active site residues of AtDAP-AT and aspartate aminotransferases revealed that the PLP binding residues in AtDAP-AT are well conserved in both enzymes. However, Glu97* and Asn309* in the active site of AtDAP-AT are not found at similar positions in aspartate aminotransferases, suggesting that specific substrate recognition may require these residues from the other monomer. A malate-bound structure of AtDAP-AT allowed LL-DAP and L-glutamate to be modelled into the active site. These initial three-dimensional structures of LL-DAP-AT provide insight into its substrate specificity and catalytic mechanism.

Authors+Show Affiliations

Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

17583737

Citation

Watanabe, Nobuhiko, et al. "Crystal Structure of LL-diaminopimelate Aminotransferase From Arabidopsis Thaliana: a Recently Discovered Enzyme in the Biosynthesis of L-lysine By Plants and Chlamydia." Journal of Molecular Biology, vol. 371, no. 3, 2007, pp. 685-702.
Watanabe N, Cherney MM, van Belkum MJ, et al. Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia. J Mol Biol. 2007;371(3):685-702.
Watanabe, N., Cherney, M. M., van Belkum, M. J., Marcus, S. L., Flegel, M. D., Clay, M. D., Deyholos, M. K., Vederas, J. C., & James, M. N. (2007). Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia. Journal of Molecular Biology, 371(3), 685-702.
Watanabe N, et al. Crystal Structure of LL-diaminopimelate Aminotransferase From Arabidopsis Thaliana: a Recently Discovered Enzyme in the Biosynthesis of L-lysine By Plants and Chlamydia. J Mol Biol. 2007 Aug 17;371(3):685-702. PubMed PMID: 17583737.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia. AU - Watanabe,Nobuhiko, AU - Cherney,Maia M, AU - van Belkum,Marco J, AU - Marcus,Sandra L, AU - Flegel,Mitchel D, AU - Clay,Matthew D, AU - Deyholos,Michael K, AU - Vederas,John C, AU - James,Michael N G, Y1 - 2007/05/26/ PY - 2007/04/13/received PY - 2007/05/21/revised PY - 2007/05/22/accepted PY - 2007/6/23/pubmed PY - 2007/9/28/medline PY - 2007/6/23/entrez SP - 685 EP - 702 JF - Journal of molecular biology JO - J Mol Biol VL - 371 IS - 3 N2 - The essential biosynthetic pathway to l-Lysine in bacteria and plants is an attractive target for the development of new antibiotics or herbicides because it is absent in humans, who must acquire this amino acid in their diet. Plants use a shortcut of a bacterial pathway to l-Lysine in which the pyridoxal-5'-phosphate (PLP)-dependent enzyme ll-diaminopimelate aminotransferase (LL-DAP-AT) transforms l-tetrahydrodipicolinic acid (L-THDP) directly to LL-DAP. In addition, LL-DAP-AT was recently found in Chlamydia sp., suggesting that inhibitors of this enzyme may also be effective against such organisms. In order to understand the mechanism of this enzyme and to assist in the design of inhibitors, the three-dimensional crystal structure of LL-DAP-AT was determined at 1.95 A resolution. The cDNA sequence of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) was optimized for expression in bacteria and cloned in Escherichia coli without its leader sequence but with a C-terminal hexahistidine affinity tag to aid protein purification. The structure of AtDAP-AT was determined using the multiple-wavelength anomalous dispersion (MAD) method with a seleno-methionine derivative. AtDAP-AT is active as a homodimer with each subunit having PLP in the active site. It belongs to the family of type I fold PLP-dependent enzymes. Comparison of the active site residues of AtDAP-AT and aspartate aminotransferases revealed that the PLP binding residues in AtDAP-AT are well conserved in both enzymes. However, Glu97* and Asn309* in the active site of AtDAP-AT are not found at similar positions in aspartate aminotransferases, suggesting that specific substrate recognition may require these residues from the other monomer. A malate-bound structure of AtDAP-AT allowed LL-DAP and L-glutamate to be modelled into the active site. These initial three-dimensional structures of LL-DAP-AT provide insight into its substrate specificity and catalytic mechanism. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/17583737/Crystal_structure_of_LL_diaminopimelate_aminotransferase_from_Arabidopsis_thaliana:_a_recently_discovered_enzyme_in_the_biosynthesis_of_L_lysine_by_plants_and_Chlamydia_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-2836(07)00716-4 DB - PRIME DP - Unbound Medicine ER -