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

Journal of Molecular Biology

Volumn 313, Issue 5, 2001, Pages 1103-1116

  Griffith, Scott C ^a   Sawaya, Michael R ^a   Boutz, Daniel R ^a   Thapar, Nitika ^a   Katz, Jonathan E ^a   Clarke, Steven ^a   Yeates, Todd O ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

D amino acids; Methyltransferase; Protein isomerization; Protein repair; S adenosylmethionine

Indexed keywords

AMINO ACID; LEVO ISOASPARTYL; METHYLTRANSFERASE; S ADENOSYLMETHIONINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME BINDING; ENZYME MECHANISM; ENZYME SUBSTRATE; ISOMERISM; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; PYROCOCCUS FURIOSUS; STRUCTURE ANALYSIS;

ARCHAEA; PYROCOCCUS FURIOSUS;

EID: 0035834493     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5095     Document Type: Article

References (62)

1. Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation
2. Chemical pathways of peptide degradation. I. Deamidation of adrenocorticotropic hormone
3. Neighboring side-chain effects on asparaginyl and aspartyl degradation: An ab initio study of the relationship between peptide conformation and backbone NH acidity
4. Isoaspartate in peptides and proteins: Formation, significance, and analysis
5. Molecular aging of tubulin: Accumulation of isoaspartyl sites in vitro and in vivo
6. 2+-free calmodulin and calmodulin damaged by in vitro aging are selectively degraded by 26 S proteasomes without ubiquitination
7. The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: Hydration and sterochemical analysis
8. Isoaspartyl post-translational modification triggers autoimmune responses to self-proteins
9. Carboxyl methylation of deamidated calmodulin increases its stability in Xenopus oocyte cytoplasm. Implications for protein repair
10. A protein carboxyl methyltransfease that recognizes and repairs age-damaged peptides and proteins and participates in their repair
11. Protein carboxyl methyltransferase facilitates conversion of atypical L-isoaspartyl peptides to normal L-aspartyl peptides
12. Conversion of isoaspartyl peptides to normal peptides: Implications for the cellular repair of damaged proteins
13. Repair of spontaneously deamidated HPr phosphocarrier protein catalyzed by the L-isoaspartate (D-aspartate) O-methyltransferase
14. Accelerated racemization of aspartic acid and asparagine residues via succinimide intermediates: An ab initio theoretical exploration of mechanism
15. Recognition of D-aspartyl residues in polypeptides by the erythrocyte L- isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis
16. Molecular phylogenetics of a protein repair methyltransferase
17. Protein repair L-isoaspartyl methyltransferase in plants. Phylogenetic distribution and the accumulation of substrate proteins in aged barley seeds
18. A highly active protein repair enzyme from an extreme thermophile: The L-isoaspartyl methyltransferase from Thermotoga maritima
19. The L-isoaspartyl protein repair methyltransferase enhances survival of aging Escherichia coli subjected to secondary environmental stresses
20. Deficiency of a protein-repair enzyme results in the accumulation of altered proteins, retardation of growth, and fatal seizures in mice
21. Targeted gene disruption of the Caenorhabditis elegans L-isoaspartyl protein repair methyltransferase impairs survival of dauer stage nematodes
22. Deficiency in protein L-isoaspartyl methyltransferase results in a fatal progressive epilepsy
23. Phenotypic analysis of seizure-prone mice lacking L-isoaspartate (D-aspartate) O-methyltransferase
24. Limited accumulation of damaged proteins in L-isoaspartyl (D-aspartyl) O-methyltransferase-deficient mice
25. Methylation at D-aspartyl residues in erythrocytes: Possible step in the repair of aged membrane proteins
26. Sequence of the D-aspartyl/L-isoaspartyl protein methyltransferase from human erythrocytes. Common sequence motifs for protein, DNA, RNA, and small molecule S-adenosylmethionine-dependent methyltransferases
27. Widespread occurrence of three sequence motifs in diverse S-adenosylmethionine-dependent methyltransferases suggests a common structure for these enzymes
28. Universal catalytic domain structure of AdoMet-dependent methyltransferases
29. Structure and evolution of AdoMet-dependent methyltransferase
30. Crystal structure of protein isoaspartyl methyltransferase: A catalyst for protein repair
31. Domain swapping: Entangling alliances between proteins
32. Automated protein model building combined with iterative structure refinement
33. CCP4 suite: Programs for protein crystallography
34. Kinetic properties of bovine brain protein L-isoaspartyl methyltransferase determined using a synthetic isoaspartyl peptide substrate
35. Synthetic peptide substrates for the erythrocyte protein carboxyl methyltransferase. Detection of a new site of methylation at isomerized L-aspartyl residues
36. Automated docking using Lamarckian genetic algorithm and empirical binding free energy function
37. TOP: A new method for protein structure comparisons and similarity searches
38. Crystal structure of glycine N-methyltransferase from rat liver
39. Crystal structure of the catalytic domain of the chemotaxis receptor methylesterase, CheB
40. Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine
41. Crystal structure of catechol O-methyltransferase
42. The structure and oligomerization of the yeast arginine methyltransferase
43. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3
44. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
45. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase
46. Purification of homologous protein carboxyl methyltransferase isozymes from human and bovine erythrocytes
47. Screening for phasing atoms in protein crystallography
48. Processing of X-ray diffraction data collected in oscillation mode
49. Automated MAD and MIR structure solution
50. Advances in direct methods for protein crystallography
51. Phase combination and cross validation in iterated density-modification calculations
52. Crystallography & NMR system: A new software suite for macromolecular structure determination
53. SHELXL: High resolution refinement
54. Main-chain bond lengths and bond angles in protein structures
55. Verification of protein structures: Patterns of nonbonded atomic interactions
56. Improved methods for building protein models in electron density maps and the location of errors in these models
57. Structural elements affecting the recognition of L-isoaspartyl residues by the L-isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis
58. Rapid automated molecular replacement by evolutionary search
59. Influence of S-adenosylhomocysteine hydrolase inhibitors on S-adenosylhomocysteine and S-adenosylmethionine pool levels in L929 cells
60. ALIGN: A program to superimpose protein coordinates, accounting for insertions and deletions
61. ALSCRIPT: A tool to format multiple sequence alignments
62. SETOR: Hardware lighted three-dimensional solid model representations of macromolecules