Structural genomics of proteins from conserved biochemical pathways and processes

Current Opinion in Structural Biology

Volumn 12, Issue 3, 2002, Pages 383-391

  Burley, Stephen K ^a,b   Bonanno, Jeffrey B ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b ELI LILLY AND COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; ISOPRENOID; PROTEIN; RIBULOSE PHOSPHATE; STEROL;

CRYSTALLIZATION; GENOMICS; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; REVIEW; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY; BIOSYNTHESIS; EVOLUTION; GENETICS; METABOLISM;

ENZYMES; EVOLUTION; GENOMICS; HUMANS; METABOLISM; STEROLS;

EID: 0036600569     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00330-5     Document Type: Review

References (93)

1. Genetics, genomics, and drug discovery
2. Protein therapeutics: Promises and challenges for the 21st century
3. Comparing function and structure between entire proteomes
4. Completeness in structural genomics
5. Structural genomics programs at the US National Institute of General Medical Sciences
6. Global efforts in structural genomics
7. An overview of structural genomics
8. X-ray diffraction studies on enzymes in the glycolytic pathway
9. Combining structural genomics and enzymology: Completing the picture in metabolic pathways and enzyme active sites
10. Determination of protein function, evolution and interactions by structural genomics
11. The Protein Data Bank
12. CATH - A hierarchic classification of protein domain structures
13. The CATH Database provides insights into protein structure/function relationship
14. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
15. A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm
16. A database of protein structure families with common folding motifs
17. Touring protein fold space with Dali/FSSP
18. SCOP: A structural classification of proteins database for the investigation of sequences and structures
19. SCOP database in 2002: Refinements accommodate structural genomics
20. Surprising similarities in structure comparison
21. IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
22. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
23. Hidden Markov models in computational biology. Applications to protein modeling
24. Hidden Markov models
25. Hidden Markov models for sequence analysis: Extension and analysis of the basic method
26. Structural assignment for whole genes and genomes using the CATH domain structure database
27. The CATH protein family database: A resource for structural and functional annotation of genomes
28. The CATH extended protein-family database: Providing structural annotations for genome sequences
29. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
30. SUPFAM - A database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: Implications for structural genomics and function annotation in genomes
31. Predicting protein structure using hidden Markov models
32. Hidden Markov models for detecting remote protein homologies
33. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
34. Pfam: A comprehensive database of protein domain families based on seed alignments
35. The Pfam protein families database
36. PROSITE: A dictionary of sites and patterns in proteins
37. The PROSITE database, its status in 2002
38. Recent improvements to the SMART domain-based sequence annotation resource
39. Increased coverage of protein families with the blocks database servers
40. The InterPro database, an integrated documentation resource for protein families, domains and functional sites
41. CDD: A database of conserved domain alignments with links to domain three-dimensional structure
42. CKAAPs DB: Aconserved key amino acid positions database
43. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins
44. CKAAPs DB: A Conserved Key Amino Acid Positions DataBase
45. Structural genomics of enzymes involved in steroid/isoprenoid biosynthesis
46. Protein structure comparison by alignment of distance matrices
47. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
48. MODBASE, a database of annotated comparative protein structure models
49. Convergent evolution of similar enzymatic function on different protein folds: The hexokinase, ribokinase, and galactokinase families of sugar kinases
50. Structure and mechanism of homoserine kinase: Prototype for the GHMP kinase superfamily
51. Structural basis for the catalysis and substrate specificity of homoserine kinase
52. On the evolution of biochemical syntheses
53. Biosynthesis of isoprenoids via mevalonate in Archaea: The lost pathway
54. The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways
55. Identification, evolution, and essentiality of the mevalonate pathway for isopentenyl diphosphate biosynthesis in Gram-positive cocci
56. An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190
57. Studies on the nonmevalonate terpene biosynthetic pathway: Metabolic role of IspH (LytB) protein
58. Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase
59. Eubacterial diterpene cyclase genes essential for production of the isoprenoid antibiotic terpentecin
60. Biosynthesis of napyradiomycins
61. Studies on the biosynthesis of terpenoids produced by Actinomycetes. Part 4. Formation of BE-40644 by the mevalonate and non-mevalonate pathways
62. Simultaneous operation of the mevalonate and non-mevalonate pathways in the biosynthesis of isopentenyl diphosphate in Streptomyces aeriouvifer
63. Biosynthesis of terpenoids: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase from tomato
64. Deoxyxylulose phosphate pathway to terpenoids
65. Selfish operons and speciation by gene transfer
66. Reconciling the many faces of lateral gene transfer
67. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
68. Comparative protein structure modeling of genes and genomes
69. Analysis and assessment of comparative modeling predictions in CASP4
70. Crystal structure of Streptococcus pneumoniae phosphomevalonate kinase
71. Structure of the Methanococcus jannaschii mevalonate kinase - a member of the GHMP kinase superfamily
72. The structure of a binary complex between a mammalian mevalonate kinase and ATP: Insights into the reaction mechanism and human inherited disease
73. Organization of the mevalonate kinase (MVK) gene and identification of novel mutations causing mevalonic aciduria and hyperimmunoglobulinaemia D and periodic fever syndrome
74. Molecular analysis of MVK mutations and enzymatic activity in hyper-IgD and periodic fever syndrome
75. ModBase: A database of comparative protein structure models
76. Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis
77. Structure of 4-diphosphocytidyl-2-C-methylerythritol synthetase involved in mevalonate-independent isoprenoid biosynthesis
78. Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway
79. Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids
80. Evidence of a role for LytB in the nonmevalonate pathway of isoprenoid biosynthesis
81. LytB, a novel gene of the 2-C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis in Escherichiacoli
82. Identification of gcpE as a novel gene of the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis in Escherichia coli
83. GcpE is involved in the 2-C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis in Escherichiacoli
84. The lytB gene of Escherichia coli is essential and specifies a product needed for isoprenoid biosynthesis
85. Studies on the nonmevalonate pathway to terpenes: The role of the GcpE (IspG) protein
86. Crystal structure of Pseudomonas mevalonii HMG-CoA reductase at 3.0 angstrom resolution
87. Substrate-induced closure of the flap domain in the ternary complex structures provides insights into the mechanism of catalysis by 3-hydroxy-3-methylglutaryl-CoA reductase
88. Crystal structure of the catalytic portion of human HMG-CoA reductase: Insights into regulation of activity and catalysis
89. Structural mechanism for statin inhibition of HMG-CoA reductase
90. The structure of the catalytic portion of human HMG-CoA reductase
91. Crystal structure of MJ1247 protein from M. jannaschii at 2.0 Å resolution infers a molecular function of 3-hexulose-6-phosphate isomerase
92. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): A vehicle for direct determination of three-dimensional structure
93. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation