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PDBsum entry 2dbt

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2dbt
Jmol
Contents
Protein chains
205 a.a. *
Ligands
EPE ×3
Waters ×21
* Residue conservation analysis
PDB id:
2dbt
Name: Hydrolase
Title: Crystal structure of chitinasE C from streptomyces griseus hut6037
Structure: ChitinasE C. Chain: a, b, c. Fragment: residues 30-294. Synonym: glycosyl hydrolase. Engineered: yes
Source: Streptomyces griseus. Organism_taxid: 1911. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
3.14Å     R-factor:   0.176     R-free:   0.225
Authors: Y.Kezuka,T.Watanabe,T.Nonaka
Key ref:
Y.Kezuka et al. (2006). Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037. J Mol Biol, 358, 472-484. PubMed id: 16516924 DOI: 10.1016/j.jmb.2006.02.013
Date:
16-Dec-05     Release date:   28-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O50152  (O50152_STRGR) -  Chitinase C
Seq:
Struc:
294 a.a.
205 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     carbohydrate binding     3 terms  

 

 
DOI no: 10.1016/j.jmb.2006.02.013 J Mol Biol 358:472-484 (2006)
PubMed id: 16516924  
 
 
Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037.
Y.Kezuka, M.Ohishi, Y.Itoh, J.Watanabe, M.Mitsutomi, T.Watanabe, T.Nonaka.
 
  ABSTRACT  
 
Chitinase C (ChiC) from Streptomyces griseus HUT6037 was the first glycoside hydrolase family 19 chitinase that was found in an organism other than higher plants. An N-terminal chitin-binding domain and a C-terminal catalytic domain connected by a linker peptide constitute ChiC. We determined the crystal structure of full-length ChiC, which is the only representative of the two-domain chitinases in the family. The catalytic domain has an alpha-helix-rich fold with a deep cleft containing a catalytic site, and lacks three loops on the domain surface compared with the catalytic domain of plant chitinases. The chitin-binding domain is an all-beta protein with two tryptophan residues (Trp59 and Trp60) aligned on the surface. We suggest the binding mechanism of tri-N-acetylchitotriose onto the chitin-binding domain on the basis of molecular dynamics (MD) simulations. In this mechanism, the ligand molecule binds well on the surface-exposed binding site through two stacking interactions and two hydrogen bonds and only Trp59 and Trp60 are involved in the binding. Furthermore, the flexibility of the Trp60 side-chain, which may be involved in adjusting the binding surface to fit the surface of crystalline chitin by the rotation of chi2 angle, is shown.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overall structure of ChiC (chain B of form I crystal). Two catalytic residues, two surface-exposed aromatic residues, and all cysteine residues are indicated by ball-and-stick drawings. No electron density can be seen in the region corresponding to Thr80 to Asn89 (TGGEGPGGNN) of chain B of the form I crystal (shown by a dotted line). The distance between the C^a atoms of Gly79 and Gly90 is 28.3 Å, and the approximate maximum dimension of the molecule is 80 Å. CatD[ChiC] has four cysteine residues that form two disulfide bonds (Cys166-Cys174 and Cys262 -Cys294) that correspond to those of barley chitinase (Cys97-Cys105 and Cys204-Cys236).
Figure 4.
Figure 4. Interactions between ChBD[ChiC] and tri-N-acetylchitotriose. The ligand molecule is well bound on the binding site by two stacking interactions (Trp59-NAG1 and Trp60-NAG3) and two hydrogen bonds (between Trp60-N and NAG2-O7 (carbonyl moiety of N-acetyl group of NAG2) and Trp59-NE1 and NAG2-O6). Hydrogen bonds are indicated by broken lines. Only Trp59 and Trp60 are responsible for the interactions.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 472-484) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21342462 J.F.Martín, A.Sola-Landa, F.Santos-Beneit, L.T.Fernández-Martínez, C.Prieto, and A.Rodríguez-García (2011).
Cross-talk of global nutritional regulators in the control of primary and secondary metabolism in Streptomyces.
  Microb Biotechnol, 4, 165-174.  
21367878 T.Taira, Y.Mahoe, N.Kawamoto, S.Onaga, H.Iwasaki, T.Ohnuma, and T.Fukamizo (2011).
Cloning and characterization of a small family 19 chitinase from moss (Bryum coronatum).
  Glycobiology, 21, 644-654.  
20480157 N.A.Udaya Prakash, M.Jayanthi, R.Sabarinathan, P.Kangueane, L.Mathew, and K.Sekar (2010).
Evolution, homology conservation, and identification of unique sequence signatures in GH19 family chitinases.
  J Mol Evol, 70, 466-478.  
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
19089411 F.P.Lin, H.H.Chuang, Y.H.Liu, C.Y.Hsieh, P.W.Lin, and H.Y.Lin (2009).
Effects of C-terminal amino acids truncation on enzyme properties of Aeromonas caviae D1 chitinase.
  Arch Microbiol, 191, 265-273.  
19143844 M.E.Lacombe-Harvey, T.Fukamizo, J.Gagnon, M.G.Ghinet, N.Dennhart, T.Letzel, and R.Brzezinski (2009).
Accessory active site residues of Streptomyces sp. N174 chitosanase: variations on a common theme in the lysozyme superfamily.
  FEBS J, 276, 857-869.  
19420727 N.Koizumi, S.Masuda, K.Maeda, Y.Isoda, R.Yatsunami, T.Fukui, and S.Nakamura (2009).
Additional carbohydrate-binding modules enhance the insoluble substrate-hydrolytic activity of beta-1,3-glucanase from alkaliphilic Nocardiopsis sp. F96.
  Biosci Biotechnol Biochem, 73, 1078-1082.  
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
18397326 H.H.Chuang, H.Y.Lin, and F.P.Lin (2008).
Biochemical characteristics of C-terminal region of recombinant chitinase from Bacillus licheniformis: implication of necessity for enzyme properties.
  FEBS J, 275, 2240-2254.  
  18453704 J.Huet, M.Azarkan, Y.Looze, V.Villeret, and R.Wintjens (2008).
Crystallization and preliminary X-ray analysis of a family 19 glycosyl hydrolase from Carica papaya latex.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 371-374.  
18182097 M.Allhorn, A.Olsén, and M.Collin (2008).
EndoS from Streptococcus pyogenes is hydrolyzed by the cysteine proteinase SpeB and requires glutamic acid 235 and tryptophans for IgG glycan-hydrolyzing activity.
  BMC Microbiol, 8, 3.  
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
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.