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PDBsum entry 1ll4

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1ll4
Jmol
Contents
Protein chains
392 a.a. *
Ligands
NAA-NAA-AMI ×4
Waters ×100
* Residue conservation analysis
PDB id:
1ll4
Name: Hydrolase
Title: Structure of c. Immitis chitinase 1 complexed with allosamidin
Structure: Chitinase 1. Chain: a, b, c, d. Fragment: residues 36-427. Engineered: yes
Source: Coccidioides immitis. Organism_taxid: 5501. Gene: cts1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.80Å     R-factor:   0.197     R-free:   0.258
Authors: K.Bortone,A.F.Monzingo,S.Ernst,J.D.Robertus
Key ref:
K.Bortone et al. (2002). The structure of an allosamidin complex with the Coccidioides immitis chitinase defines a role for a second acid residue in substrate-assisted mechanism. J Mol Biol, 320, 293-302. PubMed id: 12079386 DOI: 10.1016/S0022-2836(02)00444-8
Date:
26-Apr-02     Release date:   25-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0CB51  (CHI1_COCPS) -  Endochitinase 1
Seq:
Struc:
427 a.a.
392 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.14  - 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   4 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1016/S0022-2836(02)00444-8 J Mol Biol 320:293-302 (2002)
PubMed id: 12079386  
 
 
The structure of an allosamidin complex with the Coccidioides immitis chitinase defines a role for a second acid residue in substrate-assisted mechanism.
K.Bortone, A.F.Monzingo, S.Ernst, J.D.Robertus.
 
  ABSTRACT  
 
Allosamidin is a known inhibitor of class 18 chitinases. We show that allosamidin is a competitive inhibitor of the fungal chitinase CiX1 from Coccidioides immitis, with a K(i) of 60 nM. We report the X-ray structure of the complex and show that upon inhibitor binding the side-chain of Asp169 rotates to form an ion pair with the oxazolinium cation. The mechanism of action is thought to involve protonation of the leaving group by Glu171 and substrate assistance by the sugar acetamido moiety to form an oxazoline-like intermediate. We converted both amino acid residues to the corresponding amide and found that each mutation effectively abolishes enzyme activity. X-ray structures show the mutant enzymes retain the basic wild-type structure and that the loss of mutant activity is due to their altered chemical properties. The high affinity of allosamidin, and its similarity to the putative reaction intermediate, suggests it is a transition state analog. This helps validate our contention that the role of Asp169 is to electrostatically stabilize the reaction transition state.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The active site of wild-type and mutant CiX1. The conformation of key active-site residues of the wild-type enzyme are shown as thin solid bonds. For reference, the position of the allosamizoline ring of allosamidin is shown in dashed lines. The conformation of the C^a trace for residues 168-172, and the side-chains of 169 and 171 for the E171Q mutant is shown as thick black bonds. The conformation of corresponding atoms of the D169N mutant is shown as thick gray bonds.
Figure 7.
Figure 7. Proposed mechanism of catalysis. The first panel, upper left, shows the arrangement of key active-site residues and a conventional b-linked saccharide. As the substrate is bound, in the upper right panel, the polysaccharide chain is rotated and bent between sugars at sites -1 and +1, facilitating a distortion of the sugar at site -1 towards a high energy boat conformation.13 Two hydrogen bonds are formed with the site -1 sugar: one between a water bound to Tyr239 and the acetoamido nitrogen atom of the sugar, and the other between the sugar O6 atom and the side-chain of Asp240. A hydrogen bond is also formed between the protonated E171 side-chain and the oxygen atom of the scissile glycolytic bond. As protonation of the leaving group (+1 site sugar) proceeds and the glycosidic bond between the sugars at -1 and +1 sites breaks, the sugar at -1 develops cationic character. This cationic character is stabilized by interaction with the -1 acetamido group, and a positively charged oxazolinium intermediate is formed. The side-chain of Asp169 rotates to form a stabilizing ion pair interaction with the cationic intermediate. A water, which may be the one displaced by the oxazolinium intermediate, then attacks the C1 atom of the intermediate resulting in the formation of the b-anomer.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 293-302) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20084296 H.Li, and L.H.Greene (2010).
Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding.
  PLoS One, 5, e8654.  
20553502 H.Tsuji, S.Nishimura, T.Inui, Y.Kado, K.Ishikawa, T.Nakamura, and K.Uegaki (2010).
Kinetic and crystallographic analyses of the catalytic domain of chitinase from Pyrococcus furiosus- the role of conserved residues in the active site.
  FEBS J, 277, 2683-2695.
PDB codes: 3a4w 3a4x 3afb
20829286 J.Yang, Z.Gan, Z.Lou, N.Tao, Q.Mi, L.Liang, Y.Sun, Y.Guo, X.Huang, C.Zou, Z.Rao, Z.Meng, and K.Q.Zhang (2010).
Crystal structure and mutagenesis analysis of chitinase CrChi1 from the nematophagous fungus Clonostachys rosea in complex with the inhibitor caffeine.
  Microbiology, 156, 3566-3574.
PDB codes: 3g6l 3g6m
19596709 M.Lienemann, H.Boer, A.Paananen, S.Cottaz, and A.Koivula (2009).
Toward understanding of carbohydrate binding and substrate specificity of a glycosyl hydrolase 18 family (GH-18) chitinase from Trichoderma harzianum.
  Glycobiology, 19, 1116-1126.  
18783954 C.Li, W.Huang, and L.X.Wang (2008).
Chemoenzymatic synthesis of N-linked neoglycoproteins through a chitinase-catalyzed transglycosylation.
  Bioorg Med Chem, 16, 8366-8372.  
17576230 F.Shirazi, M.Kulkarni, and M.V.Deshpande (2007).
A rapid and sensitive method for screening of chitinase inhibitors using Ostazin Brilliant Red labelled chitin as a substrate for chitinase assay.
  Lett Appl Microbiol, 44, 660-665.  
17576216 J.L.Pereira, E.F.Noronha, R.N.Miller, and O.L.Franco (2007).
Novel insights in the use of hydrolytic enzymes secreted by fungi with biotechnological potential.
  Lett Appl Microbiol, 44, 573-581.  
17543889 Zaheer-ul-Haq, P.Dalal, N.N.Aronson, and J.D.Madura (2007).
Family 18 chitolectins: comparison of MGP40 and HUMGP39.
  Biochem Biophys Res Commun, 359, 221-226.  
16428843 N.N.Aronson, B.A.Halloran, M.F.Alexeyev, X.E.Zhou, Y.Wang, E.J.Meehan, and L.Chen (2006).
Mutation of a conserved tryptophan in the chitin-binding cleft of Serratia marcescens chitinase A enhances transglycosylation.
  Biosci Biotechnol Biochem, 70, 243-251.
PDB code: 1rd6
16685709 S.Pyrpassopoulos, M.Vlassi, A.Tsortos, Y.Papanikolau, K.Petratos, C.E.Vorgias, and G.Nounesis (2006).
Equilibrium heat-induced denaturation of chitinase 40 from Streptomyces thermoviolaceus.
  Proteins, 64, 513-523.  
16183021 F.V.Rao, O.A.Andersen, K.A.Vora, J.A.Demartino, and D.M.van Aalten (2005).
Methylxanthine drugs are chitinase inhibitors: investigation of inhibition and binding modes.
  Chem Biol, 12, 973-980.
PDB codes: 2a3a 2a3b 2a3c 2a3e
16193156 O.A.Andersen, M.J.Dixon, I.M.Eggleston, and D.M.van Aalten (2005).
Natural product family 18 chitinase inhibitors.
  Nat Prod Rep, 22, 563-579.  
15978043 W.Suginta, A.Vongsuwan, C.Songsiriritthigul, J.Svasti, and H.Prinz (2005).
Enzymatic properties of wild-type and active site mutants of chitinase A from Vibrio carchariae, as revealed by HPLC-MS.
  FEBS J, 272, 3376-3386.  
14717693 B.Synstad, S.Gåseidnes, D.M.Van Aalten, G.Vriend, J.E.Nielsen, and V.G.Eijsink (2004).
Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.
  Eur J Biochem, 271, 253-262.  
14597613 G.Vaaje-Kolstad, A.Vasella, M.G.Peter, C.Netter, D.R.Houston, B.Westereng, B.Synstad, V.G.Eijsink, and D.M.van Aalten (2004).
Interactions of a family 18 chitinase with the designed inhibitor HM508 and its degradation product, chitobiono-delta-lactone.
  J Biol Chem, 279, 3612-3619.
PDB codes: 1ur8 1ur9
15028731 M.Collin, and V.A.Fischetti (2004).
A novel secreted endoglycosidase from Enterococcus faecalis with activity on human immunoglobulin G and ribonuclease B.
  J Biol Chem, 279, 22558-22570.  
15215600 S.Karasuda, K.Yamamoto, M.Kono, S.Sakuda, and D.Koga (2004).
Kinetic analysis of a chitinase from red sea bream, Pagrus major.
  Biosci Biotechnol Biochem, 68, 1338-1344.  
12775711 D.R.Houston, A.D.Recklies, J.C.Krupa, and D.M.van Aalten (2003).
Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes.
  J Biol Chem, 278, 30206-30212.
PDB codes: 1hjv 1hjw 1hjx
12639956 F.V.Rao, D.R.Houston, R.G.Boot, J.M.Aerts, S.Sakuda, and D.M.van Aalten (2003).
Crystal structures of allosamidin derivatives in complex with human macrophage chitinase.
  J Biol Chem, 278, 20110-20116.
PDB codes: 1hki 1hkj 1hkk 1hkm
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 codes are shown on the right.