Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 3, 2009, Pages 713-718

  Blum, Marc Michael ^a,b   Mustyakimov, Marat ^c   Rüterjans, Heinz ^a   Kehe, Kai ^d   Schoenborn, Benno P ^c   Langan, Paul ^c,e   Chen, Julian C H ^a  

^a GOETHE UNIVERSITY   (Germany)

^b Blum Scientific Services   (Germany)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d BUNDESWEHR INSTITUTE OF PHARMACOLOGY AND TOXICOLOGY   (Germany)

^e UNIVERSITY OF TOLEDO   (United States)

Author keywords

Enzyme mechanism; H D exchange

Indexed keywords

ASPARTIC ACID; CALCIUM; CALCIUM HYDROXIDE; DIISOPROPYL FLUOROPHOSPHATASE; HYDROGEN; ORGANOPHOSPHORUS COMPOUND; PHOSPHOTRIESTERASE; SOLVENT; WATER;

ARTICLE; ATOM; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CONTROLLED STUDY; CRYSTAL; CRYSTALLOGRAPHY; ENZYME ACTIVATION; HYDROGEN BOND; MAXIMUM LIKELIHOOD METHOD; MOLECULAR MECHANICS; MOLECULE; NEUTRON; NEUTRON DIFFRACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; X RAY DIFFRACTION;

BINDING SITES; CRYSTALLOGRAPHY; HYDROGEN; HYDROGEN BONDING; NEUTRON DIFFRACTION; PHOSPHORIC TRIESTER HYDROLASES; PROTEIN CONFORMATION; X-RAY DIFFRACTION;

EID: 58849161928     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0807842106     Document Type: Article

References (37)

1. Kossiakoff AA, Spencer SA (1981) Direct determination of the protonation states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases: Neutron structure of trypsin. Biochemistry 20:6462-6474.
2. Wlodawer A, Sjölin L (1983) Structure of ribonuclease A: Results of joint neutron and X-ray refinement at 2.0-A resolution. Biochemistry 22:2720-2728.
3. Katz AK, et al. (2006) Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction. Proc Natl Acad Sci USA 103:8342-8347.
4. Bennett B, et al. (2006) Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc Natl Acad Sci USA 103:18493-18498.
5. Coates L, Erskine PT, Wood SP, Myles DAA, Cooper JB (2001)Aneutron Laue diffraction study of endothiapepsin: Implications for the aspartic proteinase mechanism. Biochemistry 40:13149-13157.
6. Blakeley MP, et al. (2006) Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase-inhibitor complex. Eur Biophys J 35:577-583.
7. Meilleur F, Snell EH, van der Woerd MJ, Judge RA, Myles DAA (2006) A quasi-Laue neutron crystallographic study of D-xylose isomerase. Eur Biophys J 35:601-609.
8. Kovalevsky AY, et al. (2008) Hydrogen location in stages of an enzyme-catalyzed reaction: Time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose. Biochemistry 47:7595-7597.
9. Niimura N, et al. (2006) Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography. Cell Mol Life Sci 62:285-300.
10. Kossiakoff AA (1982) Protein dynamics investigated by the neutron diffraction-hydrogen exchange technique. Nature 296:713-721.
11. Bennett BC, Gardberg AS, Blair MD, Dealwis CG (2008) On the determinants of amide backbone exchange in proteins: A neutron crystallographic comparative study. Acta Crystallogr D 64:764-783.
12. Brünger AT, et al. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D 54:905-921.
13. Mustyakimov M, Langan P (2007) Copyright C-06, 104 Patch for CNS; nCNS an open source distribution patch for CNS for macromolecular structure refinement (Los Alamos National Security, Los Alamos, NM).
14. Adams PD, et al. (2002) PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D 58:1948-1954.
15. Adams PD, et al. (2004) Recent developments in the PHENIX software for automated crystallographic structure determination. J Synchrotron Radiat 11:53-55.
16. Hartleib J, Rüterjans H (2001) High-yield expression, purification, and characterization of the recombinant diisopropylfluorophosphatase from Loligo vulgaris. Protein Expr Purif 21:210-219.
17. Scharff EI, Koepke J, Fritzsch G, Lücke C, Rüterjans H (2001) Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. Structure 9:493-502.
18. Hartleib J, Geschwindner S, Scharff EI, Rüterjans H (2001) Role of calcium ions in the structure and function of the di-isopropylfluorophosphatase from Loligo vulgaris. Biochem J 353:579-589.
19. Blum MM, Loehr F, Richardt A, Rüterjans H, Chen JCH (2006) Binding of a designed substrate analogue to diisopropyl fluorophosphatase: Implications for the phosphotriesterase mechanism. J Am Chem Soc 128:12750-12757.
20. Tanaka Y, et al. (2007) Structural and mutational analyses of Drp35 from Staphylococcus aureus: A possible mechanism for its lactonase activity. J Biol Chem 282:5770-5780.
21. Harel M, et al. (2004) Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes. Nat Struct Mol Biol 11:412-419.
22. Yeung DT, et al. (2004) Structure/function analyses of human serum paraoxonase (HuPON1) mutants designed from a DFPase-like homology model. Biochim Biophys Acta 1702:67-77.
23. Khersonsky O, Tawfik DS (2005) Structure-reactivity studies of serum paraoxonase PON1 suggest that its native activity is lactonase. Biochemistry 44:6371-6382.
24. Koepke J, Scharff EI, Lücke C, Rüterjans H, Fritzsch G (2002) Atomic resolution crystal structure of squid ganglion DFPase. Acta Crystallogr D 58:1757-1759.
25. Koepke J, Scharff EI, Lücke C, Rüterjans H, Fritzsch G (2003) Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 Å resolution. Acta Crystallogr D 59:1744-1754.
26. Langan P, Greene G (2004) Protein crystallography with spallation neutrons: Collecting and processing wavelength-resolved Laue protein data. J Appl Crystallogr 37:253-257.
27. Wlodawer A, Hendrickson WA (1982) A procedure for joint refinement of macromolecular structures with X-ray and neutron diffraction data from single crystals. Acta Crystallogr A 38:239-247.
28. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112-122.
29. 1H back-exchange. J Biomol NMR 25:291-311.
30. Kossiakoff AA, Ultsch M, White S, Eigenbrot C (1991) Neutron structure of subtilisin BPN′: Effects of chemical environment on hydrogen-bonding geometries and the pattern of hydrogen-deuterium exchange in secondary structure elements. Biochemistry 30:1211-1221.
31. Fülöp V, Jones DT (1999) Beta propellers: Structural rigidity and functional diversity. Curr Opin Struct Biol 9:715-721.
32. McPhalen CA, Strynadka NCJ, James MNG (1991) Calcium- binding sites in proteins: A structural perspective. Adv Prot Sci 42:77-144.
33. Einspahr H, Bugg CE (1980) The geometry of calcium-water interactions in crystalline hydrates. Acta Crystallogr B 36:264-271.
34. Katz AK, Glusker JP, Markham GD, Bock CW (1998) Deprotonation of water in the presence of carboxylate and magnesium ions. J Phys Chem B 102:6342-6350.
35. Blum MM, Timperley C, Williams G, Thiermann H, Worek F (2008) Inhibitory potency against human acetylcholinesterase and enzymatic hydrolysis of fluorogenic nerve agent mimics by human paraoxonase 1 and squid diisopropyl fluorophosphatase. Biochemistry 47:5216-5224.
36. Blum MM, et al. (2007) Preliminary time-of-flight neutron diffraction study on diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris. Acta Crystallogr F 63:42-45.
37. Pflugrath JW (1999) The finer things in X-ray diffraction data collection. Acta Crystallogr D 55:1718-1725.