PDBsum entry 1jg3

Transferase

PDB id: 1jg3

Contents

Protein chains

215 a.a. *

Ligands

VAL-TYR-PRO-IAS-HIS-ALA ×2

ADN ×2

Metals

_CL ×2

_NA ×2

Waters ×210

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of a protein repair methyltransferase from pyrococcus furiosus with its l-Isoaspartyl peptide substrate.

Authors

S.C.Griffith, M.R.Sawaya, D.R.Boutz, N.Thapar, J.E.Katz, S.Clarke, T.O.Yeates.

Ref.

J Mol Biol, 2001, 313, 1103-1116. [DOI no: 10.1006/jmbi.2001.5095]

PubMed id

11700066

Abstract

Protein L-isoaspartyl (D-aspartyl) methyltransferases (EC 2.1.1.77) are found in almost all organisms. These enzymes catalyze the S-adenosylmethionine (AdoMet)-dependent methylation of isomerized and racemized aspartyl residues in age-damaged proteins as part of an essential protein repair process. Here, we report crystal structures of the repair methyltransferase at resolutions up to 1.2 A from the hyperthermophilic archaeon Pyrococcus furiosus. Refined structures include binary complexes with the active cofactor AdoMet, its reaction product S-adenosylhomocysteine (AdoHcy), and adenosine. The enzyme places the methyl-donating cofactor in a deep, electrostatically negative pocket that is shielded from solvent. Across the multiple crystal structures visualized, the presence or absence of the methyl group on the cofactor correlates with a significant conformational change in the enzyme in a loop bordering the active site, suggesting a role for motion in catalysis or cofactor exchange. We also report the structure of a ternary complex of the enzyme with adenosine and the methyl-accepting polypeptide substrate VYP(L-isoAsp)HA at 2.1 A. The substrate binds in a narrow active site cleft with three of its residues in an extended conformation, suggesting that damaged proteins may be locally denatured during the repair process in cells. Manual and computer-based docking studies on different isomers help explain how the enzyme uses steric effects to make the critical distinction between normal L-aspartyl and age-damaged L-isoaspartyl and D-aspartyl residues.

Figure 3.
Figure 3. Stereo view of a ribbon diagram of the P. furiosus Image -isoaspartyl methyltransferase. The structure shown is that of the ternary complex with adenosine in stick form and the peptide VYP( Image -isoAsp)HA in ball-and-stick form. The secondary structures are labeled as in Figure 2. This Figure was made with SETOR [62].

Figure 5.
Figure 5. A protein conformational difference between the AdoMet (red) and AdoHcy (green) complexes of the P. furiosus isoaspartyl methyltransferase. The largest coordinate differences are over 10 Å. This Figure was produced with SETOR[62].

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 313, 1103-1116) copyright 2001.