Open and closed conformation of the E. coli Purine nucleoside phosphorylase active center and implications for the catalytic mechanism

Journal of Molecular Biology

Volumn 315, Issue 3, 2002, Pages 351-371

  Koellner, Gertraud ^a   Bzowska, Agnieszka ^b   Wielgus Kutrowska, Beata ^b   Luić, Marija ^c   Steiner, Thomas ^a   Saenger, Wolfram ^a   Stȩpiński, Janusz ^b  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITY OF WARSAW   (Poland)

^c RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

Active site conformation; Catalytic mechanism; E. coli; Formycin; Purine nucleoside phosphorylase

Indexed keywords

ARGININE; ASPARAGINE; DIMER; HYDROGEN; LIGAND; NUCLEOSIDE; PURINE; PURINE NUCLEOSIDE PHOSPHORYLASE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME MECHANISM; ESCHERICHIA COLI; HYDROGEN BOND; PRIORITY JOURNAL; PROTON TRANSPORT; STRUCTURE ANALYSIS;

ESCHERICHIA COLI;

EID: 0036303728     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5211     Document Type: Article

References (59)

1. Purine nucleoside phosphorylase: A target for chemotherapy
2. Purine nucleoside phosphorylase: A target for drug design
3. Purine nucleoside phosphorylase: Properties, functions and clinical aspects
4. One third-the-sites transition-state inhibitors for purine nucleoside phosphorylase
5. Purine nucleoside phosphorylase. Kinetic mechanism of the enzyme from calf spleen
6. Purine nucleoside phosphorylase. Cataytic mechanism and transition-state analysis of the arsenolysis reaction
7. Pre-steady-state transition-state analysis of the hydrolytic reaction catalyzed by purine nucleoside phosphorylase
8. Linear free energy relationships for N(7)-substituted guanosines as substrates of calf spleen purine nucleoside phosphorylase. Possible role of N(7)-protonation as an intermediary in phosphorolysis
9. Purine nucleoside phosphorylase 2. Catalytic mechanism
10. Crystal structures of purine nucleoside phosphorylase (PNP) from Cellulomonas sp. and its implications of the molecular mechanismn of trimeric PNPs
11. Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis
12. Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 Å resolution
13. Drugs by design
14. Purine nucleoside phosphorylase from Escherichia coli and Salmonella typhimurium. Purification and some properties
15. Purine nucleoside phosphorylase from Escherichia coli and Salmonella typhimurium. Initial velocity kinetics, ligand binding and reaction mechanism
16. Binding of phosphate and sulphate anions by purine nucleoside phosphorylase from E. coli: Ligand-dependent quenching of enzyme intrinsic fluorescence
17. The crystal structure of Escherichia coli purine nucleoside phosphorylase: A comparison with the human enzyme reveals a conserved topology
18. Crystal structure of the ternary complex of E. coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (sulphate) at 2.1 Å resolution
19. Luminescence studies of formycins, its aglycone, and their N-methyl derivatives: Tautomerism, sites of protonation, and phototautomerism
20. Formycins A and B and some analogues: Selective inhibitors of bacterial (Escherichia coli) purine nucleoside phosphorylase
21. Pyrazolo[4,3-d]pyrimidine nucleosides. 9. Studies on the isomeric N-methylformycins
22. Amino-imino tautomerism of N(6)-methylformycin, a potent inhibitor of E. coli, but not mammalian, purine nucleoside phosphorylase
23. Use of site-directed mutagenesis to enhance epitope-shielding effect of covalent modification of proteins with polyethylene glycol
24. PROMOTIF - A program to identify and analyze structural motifs in proteins
25. Structural analysis of substrate binding by the molecular chaperone DnaK
26. Water-inserted α-helical segments implicate reverse turns as folding intermediates
27. Active-site and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica
28. Reactions products of acetylcholinesterase and VX reveal a mobile histidine in the catalytic triad
29. Kinetics and mechanism of the acid catalysed hydrolysis of some purine nucleosides
30. Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 Å resolution
31. Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues
32. Strange bedfellows: Interactions between acidic side-chains in proteins
33. 13C NMR
34. Titration of aspartate-85 in bacteriorhodopsin: What it says about chromophore isomerization and proton release
35. Dissection of the pH dependence of inhibitor binding energetics for an aspartic protease: Direct measurement of the protonation states of the catalytic aspartic acid residues
36. The structure of concanavalin A and its bound solvent determined with small-molecule accuracy at 0.94 Å resolution
37. A neutron Laue diffraction study of endothiapepsin: Implications for the aspartic proteinase mechanism
38. Properties of purine nucleoside phosphorylase (PNP) of mammalian and bacterial origin
39. 7-Deazapurine 2′-deoxyribofuranosides are noncleavable competitive inhibitors of Escherichia coli purine nucleoside phosphorylase (PNP)
40. Properties of two unusual, and fluorescent substrates of purine nucleoside phos-phorylase: 7-methylguanosine and 7-methylinosine
41. Differential spectrophotometry of purine compounds by means of specific enzymes. I. Determination of hydroxypurines
42. Stopped-flow and Brownian dynamics studies of electrostatic effects in the kinetics of binding of 7-methyl-GppG to the protein eIF4E
43. Oscillation data reduction program
44. The CCP4 suite: Programs for protein crystallography
45. AMoRe: An automated package for molecular replacement
46. Crystallography & NMR Systems: A new suite for macromolecular structure determination
47. Improved methods for building protein models in electron density maps and the location of errors of these models
48. Improved Fourier coefficients for maps using phases from partial structures with errors
49. Buried waters and internal cavities in proteins
50. Hydrogen bonds with π-acceptors in proteins: Frequencies and role in stabilizing local 3D structures
51. Hydrogen bonds from water molecules to aromatic acceptors in very high resolution protein crystal structures
52. Reduced surface: An efficient way to compute molecular surfaces
53. MOLSCRIPT: A programme to produce both detailed and schematic plots of protein structures
54. Traitement statistique des erreurs dans la determination des structures cristallines