Related Experiment Video

Updated: Jul 30, 2026

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD
13:34

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Published on: December 30, 2016

Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide

S C Griffith1, M R Sawaya, D R Boutz

  • 1Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles 90095-1569, USA.

Journal of Molecular Biology
|November 9, 2001
PubMed

Insights

Protein L-isoaspartyl methyltransferases repair age-damaged proteins by methylating aspartyl residues. Crystal structures reveal how these enzymes bind cofactors and substrates, distinguishing between normal and damaged aspartyl forms.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Protein L-isoaspartyl (D-aspartyl) methyltransferases (EC 2.1.1.77) are crucial for protein repair across organisms.
  • These enzymes utilize S-adenosylmethionine (AdoMet) to methylate damaged aspartyl residues, maintaining protein integrity.

Purpose of the Study:

  • To elucidate the structural mechanisms of protein repair methyltransferases from the hyperthermophilic archaeon Pyrococcus furiosus.
  • To characterize enzyme-cofactor and enzyme-substrate interactions at high resolution.

Main Methods:

  • X-ray crystallography was employed to determine the structures of the methyltransferase.
  • Structures were resolved for binary complexes with AdoMet, AdoHcy, and adenosine, as well as a ternary complex with adenosine and a polypeptide substrate.
  • Manual and computational docking studies were performed to analyze substrate binding and specificity.

Main Results:

  • Crystal structures up to 1.2 A resolution revealed a deep, negatively charged pocket for cofactor binding, shielded from solvent.
  • Conformational changes in an active site loop were observed correlating with cofactor methylation state, suggesting a role in catalysis or exchange.
  • The ternary complex structure showed the substrate VYP(L-isoAsp)HA binding in a narrow cleft with extended residues, indicating local denaturation of damaged proteins.
  • Docking studies explained the enzyme's steric discrimination between L-aspartyl, L-isoaspartyl, and D-aspartyl residues.

Conclusions:

  • The study provides high-resolution structural insights into the mechanism of protein repair methyltransferases.
  • The findings highlight the enzyme's adaptation for efficient cofactor binding, substrate recognition, and specificity for damaged aspartyl residues.

More Related Videos

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep105011:27

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase09:31

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase

Published on: September 26, 2020

Related Concept Videos

Mismatch Repair01:36

Mismatch Repair

Overview
Protein Modifications in the RER01:26

Protein Modifications in the RER

Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal sequences.
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...