PDBsum entry 3ei7

Transferase

PDB id: 3ei7

Contents

Protein chains

412 a.a. *

Ligands

SO4 ×2

Waters ×629

* Residue conservation analysis

PDB id:

3ei7

Name:

Transferase

Title:

Crystal structure of apo-ll-diaminopimelate aminotransferase from arabidopsis thaliana (no plp)

Structure:

Ll-diaminopimelate aminotransferase. Chain: a, b. Fragment: unp residues 36 to 461. Synonym: ll-dap-aminotransferase, dap-aminotransferase, dap-at, atdap-at, protein aberrant growth and death 2. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress,thale-cress. Organism_taxid: 3702. Gene: dap, agd2, at4g33680, t16l1.170. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.99Å R-factor: 0.191 R-free: 0.229

Authors:

N.Watanabe,M.D.Clay,M.J.Van Belkum,M.M.Cherney,J.C.Vederas, M.N.G.James

Key ref:

N.Watanabe et al. (2008). Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana. J Mol Biol, 384, 1314-1329. PubMed id: 18952095 DOI: 10.1016/j.jmb.2008.10.022

Date:

15-Sep-08 Release date: 14-Oct-08

Protein chains

Q93ZN9  (DAPAT_ARATH) -  LL-diaminopimelate aminotransferase, chloroplastic from Arabidopsis thaliana

Seq: 461 a.a.

Struc: 412 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.83 - LL-diaminopimelate aminotransferase.
• Reaction: (2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2,3,4,5- tetrahydrodipicolinate + L-glutamate + H2O + H⁺
• Cofactor: Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2008.10.022

J Mol Biol 384:1314-1329 (2008)

PubMed id: 18952095

Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana.

N.Watanabe, M.D.Clay, M.J.van Belkum, M.M.Cherney, J.C.Vederas, M.N.James.

ABSTRACT

LL-Diaminopimelate aminotransferase (LL-DAP-AT), a pyridoxal phosphate (PLP)-dependent enzyme in the lysine biosynthetic pathways of plants and Chlamydia, is a potential target for the development of herbicides or antibiotics. This homodimeric enzyme converts L-tetrahydrodipicolinic acid (THDP) directly to LL-DAP using L-glutamate as the source of the amino group. Earlier, we described the 3D structures of native and malate-bound LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT). Seven additional crystal structures of AtDAP-AT and its variants are reported here as part of an investigation into the mechanism of substrate recognition and catalysis. Two structures are of AtDAP-AT with reduced external aldimine analogues: N-(5'-phosphopyridoxyl)-L-glutamate (PLP-Glu) and N-(5'-phosphopyridoxyl)- LL-Diaminopimelate (PLP-DAP) bound in the active site. Surprisingly, they reveal that both L-glutamate and LL-DAP are recognized in a very similar fashion by the same sets of amino acid residues; both molecules adopt twisted V-shaped conformations. With both substrates, the alpha-carboxylates are bound in a salt bridge with Arg404, whereas the distal carboxylates are recognized via hydrogen bonds to the well-conserved side chains of Tyr37, Tyr125 and Lys129. The distal C(varepsilon) amino group of LL-DAP is specifically recognized by several non-covalent interactions with residues from the other subunit (Asn309*, Tyr94*, Gly95*, and Glu97* (Amino acid designators followed by an asterisk (*) indicate that the residues originate in the other subunit of the dimer)) and by three bound water molecules. Two catalytically inactive variants of AtDAP-AT were created via site-directed mutagenesis of the active site lysine (K270N and K270Q). The structures of these variants permitted the observation of the unreduced external aldimines of PLP with L-glutamate and with LL-DAP in the active site, and revealed differences in the torsion angle about the PLP-substrate bond. Lastly, an apo-AtDAP-AT structure missing PLP revealed details of conformational changes induced by PLP binding and substrate entry into the active site.

Selected figure(s)

Figure 7.
Fig. 7. Two distinct conformations of Tyr364 in AtDAP-AT. (a) An overlay of the crystal structures of the native AtDAP-AT and the PLP-Glu aldimine analogue complex. The native structure is coloured yellow. The PLP-Glu aldimine analogue structure is coloured grey. Two different conformations of Tyr364 in the active site are shown. (b) An overlay of aromatic residues equivalent to Tyr364 of AtDAP-AT from the other type I fold aminotransferases. AtDAP-AT, AspAT (Ia), AspAT (Ib) and HisP-AT are represented in grey, yellow, blue and emerald green, respectively.

Figure 8.
Fig. 8. An overlay of the structures of native AtDAP-AT, K270N and K270Q variants of AtDAP-AT around active site Lys270 residue shown in line representation. The native, K270N and K270Q variants are coloured cyan, green and magenta, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 1314-1329) copyright 2008.

Figures were selected by an automated process.