1cns › Citations

Refined structure of the chitinase from barley seeds at 2.0 a resolution.

Song HK, Suh SW
Acta Crystallogr D Biol Crystallogr 52 289-98 (1996)
Cited: 17 times
EuropePMC logo PMID: 15299702

Abstract

Chitinase from barley seeds is a monomeric enzyme with 243 amino-acid residues and it plays a role as a defense protein. Its structure, previously determined at 2.8 A resolution by multiple isomorphous replacement method, is mainly alpha-helical [Hart, Monzingo, Ready, Ernst & Robertus, (1993). J. Mol. Biol. 229, 189-193]. The crystallization and preliminary X-ray data of the same enzyme in a different crystal form has been reported independently [Song, Hwang, Kim & Suh, (1993). Proteins, 17, 107-109}, the asymmetric unit of which contains two chitinase molecules. As a step toward understanding the general principles of catalysis, reported here is the structure of chitinase from barley seeds in this crystal form, as determined by molecular replacement and subsequently refined at 2.0 A resolution, with incorporation of partial data to 1.9 A (R factor of 18.9% for 31 038 unique reflections with F(o)> 2sigma(F) in the range 8.0-1.9 A). The r.m.s. deviations from ideal stereochemistry are 0.013 A for bond lengths and 1.32 degrees for bond angles. A superposition of the two independent molecules in the asymmetric unit gives an r.m.s. difference of 0.55 A for all protein atoms (0.43 and 0.74 A for main-chain and side-chain atoms, respectively). When the refined model of each chitinase molecule in the asymmetric unit is superposed with the starting model, the r.m.s. difference for all shared protein atoms is 0.99 A for molecule 1 and 0.85 A for molecule 2, respectively. Through a sequence comparison with homologous plant chitinases as well as a structural comparison with the active sites of other glycosidases, key catalytic residues have been identified and the active site has been located in the three-dimensional structure of the barley chitinase. The present structure, refined at an effective resolution of 2.0 A with incorporation of partial data to 1.9 A, represents a significant improvement in resolution compared to the previously reported model. The improved resolution has enabled the location of solvent atoms, including water molecules near the catalytic residues, in addition to the positioning of protein atoms with greater accuracy.

Articles - 1cns mentioned but not cited (4)

  1. Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Bishop JG, Dean AM, Mitchell-Olds T. Proc Natl Acad Sci U S A 97 5322-5327 (2000)
  2. Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. Chakraborty S, Minda R, Salaye L, Bhattacharjee SK, Rao BJ. PLoS One 6 e28470 (2011)
  3. Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis. Unhelkar MH, Duong VT, Enendu KN, Kelly JE, Tahir S, Butts CT, Martin RW. Biochim Biophys Acta Gen Subj 1861 636-643 (2017)
  4. Crystallographic structure of ChitA, a glycoside hydrolase family 19, plant class IV chitinase from Zea mays. Chaudet MM, Naumann TA, Price NP, Rose DR. Protein Sci 23 586-593 (2014)


Reviews citing this publication (1)

  1. Structural and functional evolution of chitinase-like proteins from plants. Kesari P, Patil DN, Kumar P, Tomar S, Sharma AK, Kumar P. Proteomics 15 1693-1705 (2015)

Articles citing this publication (12)

  1. Structural basis for autoinhibition and activation of Auto, a virulence-associated peptidoglycan hydrolase of Listeria monocytogenes. Bublitz M, Polle L, Holland C, Heinz DW, Nimtz M, Schubert WD. Mol Microbiol 71 1509-1522 (2009)
  2. Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymes. Hoell IA, Dalhus B, Heggset EB, Aspmo SI, Eijsink VG. FEBS J 273 4889-4900 (2006)
  3. Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037. Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T, Nonaka T. J Mol Biol 358 472-484 (2006)
  4. Heterologous expression of new antifungal chitinase from wheat. Singh A, Kirubakaran SI, Sakthivel N. Protein Expr Purif 56 100-109 (2007)
  5. Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Kezuka Y, Kojima M, Mizuno R, Suzuki K, Watanabe T, Nonaka T. Proteins 78 2295-2305 (2010)
  6. The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce. Ubhayasekera W, Rawat R, Ho SW, Wiweger M, Von Arnold S, Chye ML, Mowbray SL. Plant Mol Biol 71 277-289 (2009)
  7. Crystal structure and chitin oligosaccharide-binding mode of a 'loopful' family GH19 chitinase from rye, Secale cereale, seeds. Ohnuma T, Numata T, Osawa T, Inanaga H, Okazaki Y, Shinya S, Kondo K, Fukuda T, Fukamizo T. FEBS J 279 3639-3651 (2012)
  8. Crystal structures of a family 19 chitinase from Brassica juncea show flexibility of binding cleft loops. Ubhayasekera W, Tang CM, Ho SWT, Berglund G, Bergfors T, Chye ML, Mowbray SL. FEBS J 274 3695-3703 (2007)
  9. Crystal structures of the catalytic domain of a novel glycohydrolase family 23 chitinase from Ralstonia sp. A-471 reveals a unique arrangement of the catalytic residues for inverting chitin hydrolysis. Arimori T, Kawamoto N, Shinya S, Okazaki N, Nakazawa M, Miyatake K, Fukamizo T, Ueda M, Tamada T. J Biol Chem 288 18696-18706 (2013)
  10. Structure of bacteriophage SPN1S endolysin reveals an unusual two-module fold for the peptidoglycan lytic and binding activity. Park Y, Lim JA, Kong M, Ryu S, Rhee S. Mol Microbiol 92 316-325 (2014)
  11. Production in Pichia pastoris, antifungal activity and crystal structure of a class I chitinase from cowpea (Vigna unguiculata): Insights into sugar binding mode and hydrolytic action. Landim PGC, Correia TO, Silva FDA, Nepomuceno DR, Costa HPS, Pereira HM, Lobo MDP, Moreno FBMB, Brandão-Neto J, Medeiros SC, Vasconcelos IM, Oliveira JTA, Sousa BL, Barroso-Neto IL, Freire VN, Carvalho CPS, Monteiro-Moreira ACO, Grangeiro TB. Biochimie 135 89-103 (2017)
  12. Oat (Avena sativa) seed extract as an antifungal food preservative through the catalytic activity of a highly abundant class I chitinase. Sørensen HP, Madsen LS, Petersen J, Andersen JT, Hansen AM, Beck HC. Appl Biochem Biotechnol 160 1573-1584 (2010)


Related citations provided by authors (1)

  1. Crystallization and Preliminary X-Ray Crystallographic Analysis of Chitinase from Barley Seeds. Song HK, Hwang KY, Kim KK, Suh SW Proteins 17 107- (1993)

Quick links