PDBsum entry 2cin

Transferase

PDB id: 2cin

Contents

Protein chain

435 a.a. *

Ligands

PLP

Waters ×211

* Residue conservation analysis

PDB id:

2cin

Name:

Transferase

Title:

Lysine aminotransferase from m. Tuberculosis in the internal aldimine form

Structure:

L-lysine-epsilon aminotransferase. Chain: a. Synonym: l-lysine aminotransferase, lysine 6-aminotransferase. Engineered: yes. Other_details: link between a300 and a600

Source:

Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: c41.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.98Å R-factor: 0.157 R-free: 0.187

Authors:

S.M.Tripathi,R.Ramachandran

Key ref:

S.Mani Tripathi and R.Ramachandran (2006). Direct evidence for a glutamate switch necessary for substrate recognition: crystal structures of lysine epsilon-aminotransferase (Rv3290c) from Mycobacterium tuberculosis H37Rv. J Mol Biol, 362, 877-886. PubMed id: 16950391 DOI: 10.1016/j.jmb.2006.08.019

Date:

24-Mar-06 Release date: 14-Aug-06

Protein chain

P9WQ77  (LAT_MYCTU) -  L-lysine-epsilon aminotransferase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 449 a.a.

Struc: 435 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.36 - L-lysine 6-transaminase.
• Pathway: Lysine catabolism
• Reaction: L-lysine + 2-oxoglutarate = (S)-2-amino-6-oxohexanoate + L-glutamate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1016/j.jmb.2006.08.019

J Mol Biol 362:877-886 (2006)

PubMed id: 16950391

Direct evidence for a glutamate switch necessary for substrate recognition: crystal structures of lysine epsilon-aminotransferase (Rv3290c) from Mycobacterium tuberculosis H37Rv.

S.Mani Tripathi, R.Ramachandran.

ABSTRACT

Lysine epsilon-aminotransferase (LAT) is a PLP-dependent enzyme that is highly up-regulated in nutrient-starved tuberculosis models. It catalyzes an overall reaction involving the transfer of the epsilon-amino group of L-lysine to alpha-ketoglutarate to yield L-glutamate and alpha-aminoadipate-delta-semialdehyde. We have cloned and characterized the enzyme from Mycobacterium tuberculosisH37Rv. We report here the crystal structures of the enzyme, the first from any source, in the unliganded form, external aldimine with L-lysine, with bound PMP and with its C5 substrate alpha-ketoglutarate. In addition to interaction details in the active site, the structures reveal a Glu243 "switch" through which the enzyme changes substrate specificities. The unique substrate L-lysine is recognized specifically when Glu243 maintains a salt-bridge with Arg422. On the other hand, the binding of the common C5 substrates L-glutamate and alpha-ketoglutarate is enabled when Glu243 switches away and unshields Arg422. The structures reported here, sequence conservation and earlier mutational studies suggest that the "glutamate switch" is an elegant solution devised by a subgroup of fold type I aminotransferases for recognition of structurally diverse substrates in the same binding site and provides for reaction specificity.

Selected figure(s)

Figure 1.

Figure 2.
Figure 2. (a) The active site interactions shown in split-stereo. An external aldimine with l-lysine and (b) α-ketoglutarate-bound crystals. Oxygen and nitrogen atoms are depicted in red and blue, respectively, for the protein and ligands/cofactor. Carbon atoms from the same subunit are colored yellow while those of the dimeric counterpart are colored green. Carbon atoms of the co-factor/ligand are in pink, while water oxygen atoms are shown as cyan balls. Polar interactions are depicted by dotted lines. The movement of E243 on binding α-ketoglutarate is indicated by a curved arrow (c) Superposition of the active sites in PMP bound, l-lysine bound, α-ketoglutarate bound and internal aldimine forms. The protein chains in the respective structures are colored green, blue, yellow and pink, while the modeled glutamate is indicated in red. The Glu243 switch is indicated by a bold arrow. The movement of the PLP moiety between the unliganded and liganded forms is shown by a dotted arrow. A dotted circle indicates that the O-5 of α-ketoglutarate and N of the modeled glutamate have the correct spatial disposition to form an external aldimine with PLP. Crosses represent water molecules in the different crystal forms.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 362, 877-886) copyright 2006.

Figures were selected by an automated process.