PDBsum entry 1cns

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Anti-fungal protein PDB id
Protein chains
243 a.a. *
Waters ×226
* Residue conservation analysis
PDB id:
Name: Anti-fungal protein
Title: Crystal structure of chitinase at 1.91a resolution
Structure: Chitinase. Chain: a, b. Ec:
Source: Hordeum vulgare. Organism_taxid: 4513. Organ: seed. Tissue: seeds
1.91Å     R-factor:   0.186     R-free:   0.244
Authors: H.K.Song,S.W.Suh
Key ref:
H.K.Song and S.W.Suh (1996). Refined structure of the chitinase from barley seeds at 2.0 a resolution. Acta Crystallogr D Biol Crystallogr, 52, 289-298. PubMed id: 15299702 DOI: 10.1107/S0907444995009061
24-Jun-95     Release date:   29-Jan-96    
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Protein chains
Pfam   ArchSchema ?
P23951  (CHI2_HORVU) -  26 kDa endochitinase 2
266 a.a.
243 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Chitinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     hydrolase activity     3 terms  


DOI no: 10.1107/S0907444995009061 Acta Crystallogr D Biol Crystallogr 52:289-298 (1996)
PubMed id: 15299702  
Refined structure of the chitinase from barley seeds at 2.0 a resolution.
H.K.Song, S.W.Suh.
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.
  Selected figure(s)  
Figure 4.
Fig. 4. Stereo diagram showing the superposition of Cc~ tms in the two independent molecules i the asymmetric uni. Thick and thin lines represent molecules 1 and 2 in the asymmetric unit, respectively. Every 20th residue is labeled.
Figure 8.
Fig. 8. Amino-acid sequence alignment of 11 plant chitinases. Nine basic chiinases [from barley (BCH), ice (Ory), mouse-ear cress (Ara), rape (Bra), tomato (Lys), tobacco (Tob), kidney bean (Pha), potato (Sol), garden bean (Pea)] and two acdic chitinases [from petunia (Pet), western balsam poplar (Pop)] are aligned. Our assignment of the secondary structural elements of barley chitinase is also given [H and G represen c~- and 310- helices, respectively ] The numbering system is for the amino-acid sequence of BCH deduced from the nucleotide secuence. Residues conserved in all 11 sequences are in bold. In addition, the numbe of mismatches up to two is given below the sequence for highly conserved residues.
Figure 10.
Fig. 10. The negatively charged or polar residues, except histidine, around the catalytic residue Glu67 in molecule 1 The distances from the carboxylate C atom of Glu67 are given. Water molecules within 6 A from carboxylate C atom of Glu67 also shown as x.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 289-298) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19224400 H.P.Sørensen, L.S.Madsen, J.Petersen, J.T.Andersen, A.M.Hansen, and H.C.Beck (2010).
Oat (Avena sativa) seed extract as an antifungal food preservative through the catalytic activity of a highly abundant class I chitinase.
  Appl Biochem Biotechnol, 160, 1573-1584.  
20544965 Y.Kezuka, M.Kojima, R.Mizuno, K.Suzuki, T.Watanabe, and T.Nonaka (2010).
Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.
  Proteins, 78, 2295-2305.
PDB code: 3iwr
19210622 M.Bublitz, L.Polle, C.Holland, D.W.Heinz, M.Nimtz, and W.D.Schubert (2009).
Structural basis for autoinhibition and activation of Auto, a virulence-associated peptidoglycan hydrolase of Listeria monocytogenes.
  Mol Microbiol, 71, 1509-1522.
PDB code: 3fi7
19629717 W.Ubhayasekera, R.Rawat, S.W.Ho, M.Wiweger, S.Von Arnold, M.L.Chye, and S.L.Mowbray (2009).
The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce.
  Plant Mol Biol, 71, 277-289.
PDB codes: 3hbd 3hbe 3hbh
17608716 W.Ubhayasekera, C.M.Tang, S.W.Ho, G.Berglund, T.Bergfors, M.L.Chye, and S.L.Mowbray (2007).
Crystal structures of a family 19 chitinase from Brassica juncea show flexibility of binding cleft loops.
  FEBS J, 274, 3695-3703.
PDB codes: 2z37 2z38 2z39
17010167 I.A.Hoell, B.Dalhus, E.B.Heggset, S.I.Aspmo, and V.G.Eijsink (2006).
Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymes.
  FEBS J, 273, 4889-4900.
PDB code: 2cjl
10521473 J.Saito, A.Kita, Y.Higuchi, Y.Nagata, A.Ando, and K.Miki (1999).
Crystal structure of chitosanase from Bacillus circulans MH-K1 at 1.6-A resolution and its substrate recognition mechanism.
  J Biol Chem, 274, 30818-30825.
PDB code: 1qgi
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.