First Principles Computational Study of the Active Site of Arginase

Proteins: Structure, Function and Genetics

Volumn 54, Issue 1, 2004, Pages 1-7

  Ivanov, Ivaylo N ^a   Klein, Michael L ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Arginase; Binuclear metalloenzyme; Density functional theory; Manganese; Second shell ligands

Indexed keywords

ARGINASE; ARGININE; HYDROXIDE; LIGAND; MANGANESE; METAL;

AB INITIO CALCULATION; ANIMAL; ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONTROLLED STUDY; DENSITY; ELECTRICITY; HYDROLYSIS; METABOLISM; MOLECULAR SIZE; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; RAT; THEORETICAL MODEL;

ANIMALS; ARGINASE; ARGININE; BINDING SITES; COMPUTATIONAL BIOLOGY; HYDROLYSIS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; RATS;

EID: 0347417010     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10572     Document Type: Article

References (32)

1. Wilcox DE. Binuclear metallohydrolases. Chem Rev 1996;96:2435-2458.
2. Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J. Structures of ternary complexes of rat DNA polymerase b, a DNA template-primer and ddCTP. Science 1994;264:1891-1903.
3. Klabunde T, Sträter N, Fröhlich R, Witzel H, Krebs B. Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures. J Mol Biol 1996;259:737-748.
4. Kim EE, Wyckoff HW. Reaction mechanism of alkaline phosphatase based on crystal structures. J Mol Biol 1991;218:449-464.
5. Sträter N, Lipscomb WN. Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography. Biochemistry 1995;34:14792-14800.
6. Wilce MCJ, Bond HS, Dixon NE, Freeman HC, Guss JM, Lilley PE, Wilce JA. Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. Proc Natl Acad Sci USA 1998;95:3472-3477.
7. Jordan A, Reichard P. Ribonucletide reductases. Annu Rev Biochem 1999;67:71-98.
8. Wallar BJ, Lipscomb JD. Dioxygen activation by enzymes containing binuclear non-heme iron clusters. Chem Rev 1996;96:2625-2657.
9. Barynin V, Whittaker MM, Antonyuk SV, Lamzin VS, Harrison PM, Artymiuk PJ, Whittaker JW. Crystal structure of manganese catalase from Lactobacillus plantarum. Structure 2001;9:725-738.
10. Christianson DW. Structural chemistry and biology of manganese metalloenzymes. Prog Biophys Mol Biol 1997;67:217-243.
11. Christianson DW, Cox JD. Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes. Annu Rev Biochem 1999;68:33-57.
12. Ash DE, Cox JD, Christianson DW. Arginase: a binuclear manganese metalloenzyme. Metal Ions Biol Syst 2000;37:407-428.
13. Kanyo ZF, Scolnick LR, Ash DE, Christianson DW. Structure of a unique binuclear manganese cluster in arginase. Nature 1996;383:554-557.
14. Khangulov SV, Sossong TM, Ash DE, Dismukes GC. L-arginine binding to liver arginase requires proton transfer to gateway residue His141and coordination of the guanidinium group to the dimanganese(II,II) center. Biochemistry 1998;37:8539-8550.
15. Scolnick LR, Kanyo ZF, Cavalli RC, Ash DE, Christianson DW. Altering the binuclear manganese cluster of arginase diminishes thermostability and catalytic function. Biochemistry 1997;36:10558-10565.
16. Khangulov SV, Pessiki PJ, Barynin VV, Ash DE, Dismukes GC. Determination of the metal-ion separation and energies of the 3 lowest electronic states of dimanganese (II,II) complexes and enzymes-catalase and liver arginase. Biochemistry 1995;34:2015-2025.
17. Stemmler TL, Sossong TM, Goldstein JI, Ash DE, Elgren TE, Krutz DM, PennerHahn JE. EXAFS comparison of the dimanganese core structures of manganese catalase, arginase, and manganese-substituted ribonucleotide reductase and hemerythrin. Biochemistry 1997;36:9847-9858.
18. Lee D, Hung PL, Spingler B, Lippard SJ. Sterically hindered carboxylate ligands support water-bridged dimetallic centers that model features of metallohydrolase active sites. Inorg Chem 2002;4:521-531.
19. Cama E, Colleluori DM, Emig FA, Shin H, Kim SW, Kim NN, Traish AM, Ash DE, Christianson DW. Human arginase II: Crystal structure and physiological role in male and female sexual arousal. Biochemistry 2003;42:8445-8451.
20. Cox JD, Cama E, Colleluori DM, Pethe S, Boucher JL, Mansuy D, Ash DE, Christianson DW. Mechanistic and metabolic inferences from the binding of substrate analogues and products to arginase. Biochemistry 2001;40:2689-2701.
21. Cama E, Ernig FA, Ash DE, Christianson DW. Structural and functional importance of first-shell metal ligands in the binuclear manganese cluster of arginase I. Biochemistry 2003;42:7748-7758.
22. Car R, Parrinello M. Unified approach for molecular-dynamics and density-functional theory. Phys Rev Lett 1985;55:2471-2474.
23. Hutter J, Alavi A, Deutsch T, Bernasconi M, Goedecker S, Marx D, Tuckerman M, Parrinello M. CPMD version 3.4. Stuttgart and Zurich: MPI für Fëstkörperforschung and IBM Research Laboratory; 1995-2000.
24. Perdew JP. Density-functional approximation for the correlation-energy of the inhomogeneous electron-gas. Phys Rev B 1986;33:8822-8824.
25. Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 1988;38:3098-3100.
26. Troullier N, Martins JL. Efficient pseudopotentials for plane-wave calculations. Phys Rev B 1991;43:1993-2006.
27. Hockney RW. The potential calculation and some applications. Methods Comput Phys 1970;9:135-211.
28. Siegbahn PEM. Quantum chemical studies of manganese centers in biology. Curr Opin Chem Biol 2002;6:227-235.
29. Blomberg MRA, Siegbahn PEM. A quantum chemical approach to the study of reaction mechanisms of redox-active metalloenzymes. J Phys Chem B 2001;105:9375-9386.
30. Lee CT, Yang WT, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density. Phys Rev B 1988;37:785-789.
31. Godbout N, Salahub DR, Andzelm J, Wimmer E. Optimization of Gaussian type basis sets for local spin-density functional calculations: 1. Boron through neon, optimization technique and validation. Can J Chem 1992;70:560-571.
32. High Performance Computational Chemistry Group. NWChem, a computational chemistry package for parallel computers, Version 4.1. Richland, WA: Pacific Northwest National Laboratory; 2002.