Evolution of function in protein superfamilies, from a structural perspective

Journal of Molecular Biology

Volumn 307, Issue 4, 2001, Pages 1113-1143

  Todd, Annabel E ^a   Orengo, Christine A ^a   Thornton, Janet M ^a,b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Diversity; Enzyme superfamilies; Evolution; Function; Three dimensional structure

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

EID: 0035815113     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4513     Document Type: Article

References (113)

1. Crystal structure of 2-oxoisovalerate dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes
2. Evolutionary relationships among pyridoxal-5′-phosphate-dependent enzymes
3. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
4. The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold
5. A polymerase I palm in adenylyl cyclase?
6. Fly Base: The Drosophila genetic database
7. Understanding enzyme superfamilies - Chemistry as the fundamental determinant in the evolution of new catalytic activities
8. The enzyme database in 2000
9. The SWISS-PROT protein sequence database and its supplement trEMBL in 2000
10. Electron density map of apoferritin at 2.8 Å resolution
11. Classification of peptidases
12. The Pfam protein families database
13. Structure of the hexapeptide xenobiotic acetyltransferase from Pseudomonas aervginosa
14. The Protein Data Bank: A computer-based archival file for macro-molecular structures
15. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis
16. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate
17. Structure of bovine pancreatic cholesterol esterase at 1.6 Å: Novel structural features involved in lipase activation
18. The structure of flavocytochrome-c sulfide dehydrogenase from a purple phototrophic bacterium
19. Proteins - 1000 families for the molecular biologist
20. The 1.8 Å crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity
21. 8 barrels: Implications for the evolution of metabolic pathways
22. Practical limits of function prediction
23. The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid
24. Ferritin: Design and formation of an iron-storage molecule
25. Flavoenzymes: Diverse catalysts with recurrent features
26. Analogous enzymes: Independent inventions in enzyme evolution
27. Aldolases of the DhnA family: A possible solution to the problem of pentose and hexose biosynthesis in Archaea
28. Mechanistically diverse enzyme superfamilies: The importance of chemistry in the evolution of catalysis
29. The crystal structure of Dps, a ferritin homolog that binds and protects DNA
30. Two tricks in one bundle: Helixturn-helix gains enzymatic activity
31. MutY catalytic core, mutant and bound adenine structures define specificity for DNA
32. Catalytic reactivities and structure/function relationships of cytochrome P490 enzymes
33. The crystal-structure of benzoylformate decarboxylase at 1.6 Angstrom resolution: Diversity of catalytic residues in thiamin diphosphate-dependent enzymes
34. Evolution of an enzyme-active site: The structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase
35. The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
36. Of barn owls and bankers: A lush variety of α/β hydrolases
37. A classification of glycosyl hydrolases based on amino-acid-sequence similarities
38. Crystal structure determination, refinement and molecular model of creatine amidinohydrolase from Pseudomonas putida
39. Mapping the protein universe
40. 2 multienzyme complex from Salmonella typhimurivm
41. Evaluation of functionally important amino acids in L-aspartate ammonia-lyase from Escherichia coli
42. Moonlighting proteins
43. Enzyme recruitment in evolution of new function
44. Crystal structure of transaldolase B from Escherichia coli suggests a circular permutation of the α/β barrel within the class I aldolase family
45. Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between β-galactosidase and other glycohydrolases
46. Three-dimensional structure of phosphoenolpyruvate carboxylase: A proposed mechanism for allosteric inhibition
47. MOLSCRIPT - A program to produce both detailed and schematic plots of protein structures
48. Convergent evolution of similar function in two structurally divergent enzymes
49. PDBsum: A web-based database of summaries and analyses of all PDB structures
50. Identification of non-heme diiron proteins that catalyze triple bond and epoxy group formation
51. The structure of SAICAR synthase: An enzyme in the de novo pathway of purine nucleotide biosynthesis
52. Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: Stereochemical analysis
53. Insights into the mechanism of Escherichia coli methionine aininopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues
54. The Zn-peptidase superfamily: Functional convergence after evolutionary divergence
55. Protein folds and functions
56. Thioredoxin - A fold for all reasons
57. DNA repair mechanisms for the recognition and removal of damaged DNA bases
58. A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase
59. Structural comparison of cupredoxin domains: Domain recycling to construct proteins with novel functions
60. Can homologous proteins evolve different enzymatic activities
61. Structural classification of proteins: New superfamilies
62. How far divergent evolution goes in proteins
63. SCOP - A structural classification of proteins database for the investigation of sequences and structures
64. α/β hydrolase fold enzymes: The family keeps growing
65. Identification and characterisation of the two functional domains in cytochrome P450 BM-3, a catalytically self-sufficient monooxygenase induced by barbituates in Bacillus megaterium
66. A general method applicable to the search for similarities in the amino acid sequence of two proteins
67. Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: Catalytic roles of Cys10 and His106
68. Three-dimensional structure of the free radical protein of ribonucleotide reductase
69. Catalytic promiscuity and the evolution of new enzymatic activities
70. The α/β hydrolase fold
71. CORA - Topological fingerprints for protein structural families
72. Protein superfamilies and domain superfolds
73. CATH - A hierarchic classification of protein domain structures
74. Improved tools for biological sequence comparison
75. Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold
76. Dèja vu all over again
77. On the origin of enzymatic species
78. The recruitment of crystallins - New functions precede gene duplication
79. Molecular cloning of the β-subunit of human prolyl-4-hydroxylase. This subunit and protein disulphide isomerase are products of the same gene
80. Molecular basis of glutathione synthetase deficiency and a rare gene permutation event
81. Cytochrome P450
82. A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units
83. Circular permutations in proteins
84. Protein fold irregularities that hinder sequence analysis
85. Supersites within superfolds. Binding site similarity in the absence of homology
86. Evolution of protein complexity - The blue copper-containing oxidases and related proteins
87. Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes
88. Pancreatic lipases - Evolutionary intermediates in a positional change of catalytic carboxylates
89. Redesigning the active-site of Geotrichum-candidum lipase
90. The structure of avian eye lens δ-crystallin reveals a new fold for a superfamily of oligomeric enzymes
91. Protein structure alignment
92. Stereochemistry of chitin hydrolysis by a plant chitinase lysozyme and X-ray structure of a complex with allosamidin - Evidence for substrate assisted catalysis
93. The 1.8 Angstrom resolution structure of hevamine, a plant chitinase/lysozyme, and analysis of the conserved sequence and structure motifs of glycosyl hydrolase family 18
94. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure
95. Structure of carbamoyl phosphate synthase: A journey of 96 Å from substrate to product
96. Crystal-structure of Escherichia coli QOR quinone oxidoreductase complexed with NADPH
97. Covalent structure of the flavoprotein subunit of the flavocytochrome c: Sulfide dehydrogenase from the purple phototrophic bacterium Chromatium vinosum
98. Crystal-structure of endo-β-N-acetylglucosarninidase F1, an α/β-barrel enzyme adapted for a complex substrate
99. A test case for structure-based functional assignment: The 1.2 Angstrom crystal structure of the yjgF gene product from Escherichia coli
100. Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase
101. Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
102. Crystal structure of calsequestrin from rabbit skeletal muscle sarcoplasmic reticulum
103. Protein disulphide isomerase is a component of the microsomal triglyceride transfer protein complex
104. Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: Indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 Å resolution
105. Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
106. Recruitment of enzymes as lens structural proteins
107. Structural and functional-relationships between fumarase and aspartase - Nucleotide-sequences of the fumarase (fumC) and aspartase (aspA) genes of Escherichia coli-K12
108. Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase
109. The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase - Chemical modification and site-directed mutagenesis
110. Crystal structure of Escherichia coli HdeA
111. Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics
112. From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions