Crystal structure determination and inhibition studies of a novel xylanase and α-amylase inhibitor protein (XAIP) from Scadoxus multiflorus

FEBS Journal

Volumn 277, Issue 13, 2010, Pages 2868-2882

  Kumar, Sanjit ^a   Singh, Nagendra ^a   Sinha, Mau ^a   Dube, Divya ^a   Singh, S Baskar ^a   Bhushan, Asha ^a   Kaur, Punit ^a   Srinivasan, Alagiri ^a   Sharma, Sujata ^a   Singh, Tej P ^a  

^a ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

Amylase; Crystal structure; Enzyme inhibition; TIM barrel fold; Xylanase

Indexed keywords

AMYLASE; AMYLASE INHIBITOR; CARBOHYDRATE BINDING PROTEIN; HELIX LOOP HELIX PROTEIN; POLYPEPTIDE; PROTEIN; PROTEIN XAIP; TRIOSEPHOSPHATE ISOMERASE; UNCLASSIFIED DRUG; XYLAN ENDO 1,3 BETA XYLOSIDASE;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; ENZYME INHIBITION; MOLECULAR DOCKING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN ISOLATION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

ALPHA-AMYLASES; AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ENDO-1,4-BETA XYLANASES; ENZYME INHIBITORS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; PLANT ROOTS; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

SCADOXUS MULTIFLORUS;

EID: 77953599240     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2010.07703.x     Document Type: Article

References (42)

1. Juge N (2006) Plant protein inhibitors of cell wall degrading enzymes. Trends Plant Sci 11, 359-367.
2. Lebeda A, Luhova L, Sedlarova M Jancova D (2001) The role of enzymes in plant-fungal pathogen interactions. Z Pflanzenk Pflanzens J Plant Dis Prot 108, 89 111.
3. Misas-Villamil JC van der Hoorn RA (2008) Enzyme-inhibitor interactions at the plant-pathogen interface. Curr Opin Struct Biol 11, 380-388.
4. Bugbee WM (1993) A pectin lyase inhibitor protein from cell-walls of sugar-beet. Phytopathology 83, 63-68.
5. Mclauchlan WR, Garcia-Conesa MT, Williamson G, Roza M, Ravestein P Maat J (1999) A novel class of protein from wheat which inhibits xylanases. Biochem J 338, 441-446.
6. Gebruers K, Brijs K, Courtin CM, Fierens K, Goesaert H, Rabijns A, Raedschelders G, Robben J, Sansen S, Sorensen JF et al. (2004) Properties of TAXI-type endoxylanase inhibitors. Biochim Biophys Acta 1696, 213-221.
7. Matteo AD, Bonivento D, Tsernoglou D, Federici L Cervone F (2006) Polygalacturonase-inhibiting protein (PGIP) in plant defence: a structural view. Phytochemistry 67, 528-533.
8. Matteo AD, Giovane A, Raiola A, Camardella L, Bonivento D, De Lorenzo G, Cervone F, Bellincampi D Tsernoglou D (2005) Structural basis for the interaction between pectin methylesterase and a specific inhibitor protein. Plant Cell 17, 849-859.
9. Payan F, Leone P, Porciero S, Furniss C, Tahir T, Williamson G, Durand A, Manzanares P, Gilbert HJ, Juge N et al. (2004) The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases. J Biol Chem 279, 36029-36037.
10. Vanscheltinga ACT, Hennig M Dijkstra BW (1996) The 1.8 ̊ resolution structure of hevamine, a plant chitinase/lysozyme, and analysis of the conserved sequence and structure motifs of glycosyl hydrolase family 18. J Mol Biol 262, 243-257.
11. Hennig M, Jansonius JN, Vanscheltinga ACT, Dijkstra BW Schlesier B (1995) Crystal structure of concanavalin B at 1.65 ̊ resolution. An 'inactivated' chitinase from seeds of Canavalia ensiformis. J Mol Biol 254, 237-246.
12. Hennig M, Pfeffer-Hennig S, Dauter Z, Wilson KS, Schlesier B Nong VH (1995) Crystal structure of narbonin at 1.8 ̊ resolution. Acta Crystallogr Sect D: Biol Crystallogr 51, 177-189.
13. Payan F, Flatman R, Porciero S, Williamson G, Juge N Roussel A (2003) Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum var. Soisson). Biochem J 372, 399-405.
14. Kengo K Haruki N (2003) Protein informatics towards function identification. Curr Opin Struct Biol 13, 396-400.
15. Farber GK Petsko GA (1990) The evolution of α/β barrel enzymes. Trends Biochem Sci 15, 228-234.
16. Wilson KS Vorgias CE (1994) Crystal structure of a bacterial chitinase at 2.3 ̊ resolution. Structure 2, 1169-1180.
17. Hackman RH Goldberg M (1964) New substrates for use with chitinases. Anal Biochem 8, 397-401.
18. Machius M, Declerck N, Huber R Wiegand G (2003) Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface. J Biol Chem 278, 11546-11553.
19. Elliott GO, McLauchlan WR, Williamson G Kroon PA (2003) A wheat xylanase inhibitor protein (XIP-I) accumulates in the grain and has homologues in other cereals. J Cereal Sci 2, 187-194.
20. Pierleoni A, Martelli PL, Fariselli P Casadio R (2006) BaCelLo: a balanced subcellular localization predictor. Bioinformatics 22, e408 e416.
21. Yu CS, Chen YC, Lu CH Hwang JK (2006) Prediction of protein subcellular localization. Proteins: struct. funct. Bioinformatics 64, 643-651.
22. http://linux.softberry.com/berry.phtml? access date: March 10, 2010.
23. Davis WI, Leaver-Fay A, Chen BV, Block NJ, Kapral JG, Wang X, Murray WL, Arendall BW, Snoeyink J, Richardson SJ et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35, Web Server issue, W375 W383.
24. Ramachandran GN Sasisekaran V (1968) Conformation of polypeptides and proteins. Adv Protein Chem 23, 283-438.
25. Laskowski RA, MacArthur MW, Moss DS Thornton JM (1993) procheck: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26, 283-291.
26. Rao VH, Guan C van Roey P (1995) Crystal structure of endo-b-N-acetylglucosaminidase H at 1.9 ̊ resolution: active-site geometry and substrate recognition. Structure 3, 449-457.
27. Vallee F, Kadziola A, Bourne Y, Juy M, Rodenburg KW, Svensson B Haser R (1998) Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 ̊ resolution. Structure 15, 649-659.
28. Stanley D, Farnden FJK Macrae AE (2005) Plant α-amylase: functions and role in carbohydrate metabolism. Biologia (Bratis) 60, 65-71.
29. Micheelsen PO, Vévodova J, De Maria L, Ostergaard PR, Friis EP, Wilson K Skjot M (2008) Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition. J Mol Biol 380, 681-690.
30. Nielsen PK, Bønsager BC, Berland CR, Sigurskjold BW Svensson B (2003) Kinetics and energetics of the binding between barley alpha-amylase/subtilisin inhibitor and barley alpha-amylase 2 analyzed by surface plasmon resonance and isothermal titration calorimetry. Biochemistry 42, 1478-1487.
31. Sancho AI, Faulds CB, Svensson B, Bartolome B, Williamson G Juge N (2003) Cross-inhibitory activity of cereal protein inhibitors against alpha-amylases and xylanases. Biochim Biophys Acta 1650, 136-144.
32. Legrand M, Kauffmann S, Geoffroy P Fritig B (1987) Biological function of pathogenesis-related proteins: four tobacco pathogenesis-related proteins are chitinases. Proc Natl Acad Sci USA 84, 6750-6754.
33. Chomczynski P Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate phenol-chloroform extraction. Anal Biochem 162, 156-159.
34. Edman P (1949) A method for the determination of amino acid sequence in peptides. Arch Biochem 22, 475.
35. Bernfeld P (1955) Amylase alpha and beta. Methods Enzymol 1, 149-158.
36. Otwinowski Z Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326.
37. Vagin A Taplyakov A (1997) MOLREP: An automated program for molecular replacement. J Appl Crystallogr 30, 1022-1025.
38. Murshudov GN, Vagin AA Dodson EJ (1997) Refinement of protein structures by the maximum likelihood method. Acta Crystallogr Sect D: Biol Crystallogr 53, 240-255.
39. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr Sect D: Biol Crystallogr 50, 760-763.
40. Jones TA, Zou J, Cowan SW Kjeldgaard M (1991) Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr A 47, 110-118.
41. Emsley P Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D: Biol Crystallogr 60, 2126-2132.
42. DeLano WL (2002) The PyMol Molecular Graphics System. DeLano Scientific