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PDBsum entry 1hvm

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protein links
Hydrolase PDB id
1hvm
Jmol
Contents
Protein chain
273 a.a.
Waters ×249
Superseded by: 2hvm
PDB id:
1hvm
Name: Hydrolase
Structure: Hevamine a. Chain: null. Other_details: plant endochitinase/lysozyme
Source: Hevea brasiliensis. Rubber tree. Tissue: latex
Resolution:
2.20Å     R-factor:   0.169     R-free:   0.261
Authors: A.C.Terwisscha Van Scheltinga,K.H.Kalk,J.J.Beintema, B.W.Dijkstra
Key ref:
A.C.Terwisscha van Scheltinga et al. (1994). Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor. Structure, 2, 1181-1189. PubMed id: 7704528 DOI: 10.1016/S0969-2126(94)00120-0
Date:
13-Oct-94     Release date:   02-Dec-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23472  (CHLY_HEVBR) -  Hevamine-A
Seq:
Struc:
311 a.a.
273 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.14, 3.2.1.17  - Chitinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.

 

 
DOI no: 10.1016/S0969-2126(94)00120-0 Structure 2:1181-1189 (1994)
PubMed id: 7704528  
 
 
Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor.
A.C.Terwisscha van Scheltinga, K.H.Kalk, J.J.Beintema, B.W.Dijkstra.
 
  ABSTRACT  
 
BACKGROUND: Hevamine is a member of one of several families of plant chitinases and lysozymes that are important for plant defence against pathogenic bacteria and fungi. The enzyme can hydrolyze the linear polysaccharide chains of chitin and peptidoglycan. A full understanding of the structure/function relationships of chitinases might facilitate the production of transgenic plants with increased resistance towards a wide range of pathogens. RESULTS: The crystal structure of hevamine has been determined to a resolution of 2.2 A, and refined to an R-factor of 0.169. The enzyme possesses a (beta alpha)8-barrel fold. An inhibitor binding study shows that the substrate-binding cleft is located at the carboxy-terminal end of the beta-barrel, near the conserved Glu127. Glu127 is in a position to act as the catalytic proton donor, but no residue that might stabilize a positively charged oxocarbonium ion intermediate was found. A likely mechanism of substrate hydrolysis is by direct attack of a water molecule on the C1 atom of the scissile bond, resulting in inversion of the configuration at C1. CONCLUSIONS: The structure of hevamine shows a completely new lysozyme/chitinase fold and represents a new class of polysaccharide-hydrolyzing (beta alpha)8-barrel enzymes. Because the residues conserved in the family to which hevamine belongs are important for maintaining the structure of the (beta alpha)8-barrel, all members of the family, including fungal, bacterial and insect chitinases, are likely to share this architecture. The crystal structure obtained provides a basis for protein engineering studies in this family of chitinases.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Schematic drawing of the hydrogen-bonding pattern of the consensus regions. The highly conserved side chains and the hydrogen bonds that they make within the consensus regions are shown in red, the rest of the consensus regions are shown in blue. Hydrogen bonds made with residues outside the consensus regions are shown in green. Protonation of the side chains is shown to be most probable at pH 4.0, the pH optimum of hevamine. Figure 4. Schematic drawing of the hydrogen-bonding pattern of the consensus regions. The highly conserved side chains and the hydrogen bonds that they make within the consensus regions are shown in red, the rest of the consensus regions are shown in blue. Hydrogen bonds made with residues outside the consensus regions are shown in green. Protonation of the side chains is shown to be most probable at pH 4.0, the pH optimum of hevamine.
Figure 6.
Figure 6. Stereo figure showing the van der Waals interactions between hevamine and tri-NAG. Figure 6. Stereo figure showing the van der Waals interactions between hevamine and tri-NAG.
 
  The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 1181-1189) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21044846 A.W.Schüttelkopf, L.Gros, D.E.Blair, J.A.Frearson, D.M.van Aalten, and I.H.Gilbert (2010).
Acetazolamide-based fungal chitinase inhibitors.
  Bioorg Med Chem, 18, 8334-8340.
PDB code: 2xtk
21085702 A.Wohlkönig, J.Huet, Y.Looze, and R.Wintjens (2010).
Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs.
  PLoS One, 5, e15388.  
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.  
19642017 J.Zhang, Y.Sun, F.Li, B.Huang, and J.Xiang (2010).
Molecular characterization and expression analysis of chitinase (Fcchi-3) from Chinese shrimp, Fenneropenaeus chinensis.
  Mol Biol Rep, 37, 1913-1921.  
20222972 N.L.Raju, B.N.Gnanesh, P.Lekha, B.Jayashree, S.Pande, P.J.Hiremath, M.Byregowda, N.K.Singh, and R.K.Varshney (2010).
The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.).
  BMC Plant Biol, 10, 45.  
19348025 G.Vaaje-Kolstad, A.C.Bunaes, G.Mathiesen, and V.G.Eijsink (2009).
The chitinolytic system of Lactococcus lactis ssp. lactis comprises a nonprocessive chitinase and a chitin-binding protein that promotes the degradation of alpha- and beta-chitin.
  FEBS J, 276, 2402-2415.  
18975073 Y.Lü, H.Yang, H.Hu, Y.Wang, Z.Rao, and C.Jin (2009).
Mutation of Trp137 to glutamate completely removes transglycosyl activity associated with the Aspergillus fumigatus AfChiB1.
  Glycoconj J, 26, 525-534.  
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.  
18355718 H.Prinz (2008).
How to identify a pharmacophore.
  Chem Biol, 15, 207-208.  
  19204807 M.Karlsson, and J.Stenlid (2008).
Comparative Evolutionary Histories of the Fungal Chitinase Gene Family Reveal Non-Random Size Expansions and Contractions due to Adaptive Natural Selection.
  Evol Bioinform Online, 4, 47-60.  
18355729 O.A.Andersen, A.Nathubhai, M.J.Dixon, I.M.Eggleston, and D.M.van Aalten (2008).
Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin.
  Chem Biol, 15, 295-301.
PDB codes: 3ch9 3chc 3chd 3che 3chf
18342250 Q.Zhu, Y.Arakane, D.Banerjee, R.W.Beeman, K.J.Kramer, and S.Muthukrishnan (2008).
Domain organization and phylogenetic analysis of the chitinase-like family of proteins in three species of insects.
  Insect Biochem Mol Biol, 38, 452-466.  
18205958 S.Pantoom, C.Songsiriritthigul, and W.Suginta (2008).
The effects of the surface-exposed residues on the binding and hydrolytic activities of Vibrio carchariae chitinase A.
  BMC Biochem, 9, 2.  
18563407 Z.H.Liu, Q.Yang, S.Hu, J.D.Zhang, and J.Ma (2008).
Cloning and characterization of a novel chitinase gene (chi46) from Chaetomium globosum and identification of its biological activity.
  Appl Microbiol Biotechnol, 80, 241-252.  
17524989 R.Hurtado-Guerrero, and D.M.van Aalten (2007).
Structure of Saccharomyces cerevisiae chitinase 1 and screening-based discovery of potent inhibitors.
  Chem Biol, 14, 589-599.
PDB codes: 2uy2 2uy3 2uy4 2uy5
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
17156413 Y.Kwon, S.H.Kim, M.S.Jung, M.S.Kim, J.E.Oh, H.W.Ju, K.I.Kim, E.Vierling, H.Lee, and S.W.Hong (2007).
Arabidopsis hot2 encodes an endochitinase-like protein that is essential for tolerance to heat, salt and drought stresses.
  Plant J, 49, 184-193.  
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.  
16934035 B.S.Cavada, F.B.Moreno, B.A.da Rocha, W.F.de Azevedo, R.E.Castellón, G.V.Goersch, C.S.Nagano, E.P.de Souza, K.S.Nascimento, G.Radis-Baptista, P.Delatorre, Y.Leroy, M.H.Toyama, V.P.Pinto, A.H.Sampaio, D.Barettino, H.Debray, J.J.Calvete, and L.Sanz (2006).
cDNA cloning and 1.75 A crystal structure determination of PPL2, an endochitinase and N-acetylglucosamine-binding hemagglutinin from Parkia platycephala seeds.
  FEBS J, 273, 3962-3974.
PDB code: 2gsj
16541109 F.V.Rao, H.C.Dorfmueller, F.Villa, M.Allwood, I.M.Eggleston, and D.M.van Aalten (2006).
Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis.
  EMBO J, 25, 1569-1578.
PDB codes: 2cbi 2cbj
16704970 H.F.Bigg, R.Wait, A.D.Rowan, and T.E.Cawston (2006).
The mammalian chitinase-like lectin, YKL-40, binds specifically to type I collagen and modulates the rate of type I collagen fibril formation.
  J Biol Chem, 281, 21082-21095.  
16428844 K.E.Kabir, D.Hirowatari, K.Watanabe, and D.Koga (2006).
Purification and characterization of a novel isozyme of chitinase from Bombyx mori.
  Biosci Biotechnol Biochem, 70, 252-262.  
16420473 S.J.Horn, A.Sørbotten, B.Synstad, P.Sikorski, M.Sørlie, K.M.Vårum, and V.G.Eijsink (2006).
Endo/exo mechanism and processivity of family 18 chitinases produced by Serratia marcescens.
  FEBS J, 273, 491-503.  
16499618 S.S.Klemsdal, J.L.Clarke, I.A.Hoell, V.G.Eijsink, and M.B.Brurberg (2006).
Molecular cloning, characterization, and expression studies of a novel chitinase gene (ech30) from the mycoparasite Trichoderma atroviride strain P1.
  FEMS Microbiol Lett, 256, 282-289.  
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
15561707 M.B.Joshi, M.E.Rogers, A.M.Shakarian, M.Yamage, S.A.Al-Harthi, P.A.Bates, and D.M.Dwyer (2005).
Molecular characterization, expression, and in vivo analysis of LmexCht1: the chitinase of the human pathogen, Leishmania mexicana.
  J Biol Chem, 280, 3847-3861.  
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
14766598 T.Kawase, A.Saito, T.Sato, R.Kanai, T.Fujii, N.Nikaidou, K.Miyashita, and T.Watanabe (2004).
Distribution and phylogenetic analysis of family 19 chitinases in Actinobacteria.
  Appl Environ Microbiol, 70, 1135-1144.  
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
12851408 F.Fusetti, T.Pijning, K.H.Kalk, E.Bos, and B.W.Dijkstra (2003).
Crystal structure and carbohydrate-binding properties of the human cartilage glycoprotein-39.
  J Biol Chem, 278, 37753-37760.
PDB codes: 1nwr 1nws 1nwt 1nwu
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
12728996 K.Suzukawa, T.Yamagami, T.Ohnuma, H.Hirakawa, S.Kuhara, Y.Aso, and M.Ishiguro (2003).
Mutational analysis of amino acid residues involved in catalytic activity of a family 18 chitinase from tulip bulbs.
  Biosci Biotechnol Biochem, 67, 341-346.  
12554965 Y.Papanikolau, G.Tavlas, C.E.Vorgias, and K.Petratos (2003).
De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin.
  Acta Crystallogr D Biol Crystallogr, 59, 400-403.
PDB codes: 1edq 1ffq
12093900 D.R.Houston, K.Shiomi, N.Arai, S.Omura, M.G.Peter, A.Turberg, B.Synstad, V.G.Eijsink, and D.M.van Aalten (2002).
High-resolution structures of a chitinase complexed with natural product cyclopentapeptide inhibitors: mimicry of carbohydrate substrate.
  Proc Natl Acad Sci U S A, 99, 9127-9132.
PDB codes: 1h0g 1h0i
11846790 E.Bokma, H.J.Rozeboom, M.Sibbald, B.W.Dijkstra, and J.J.Beintema (2002).
Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis.
  Eur J Biochem, 269, 893-901.
PDB codes: 1kqy 1kqz 1kr0 1kr1
11960986 F.Fusetti, H.von Moeller, D.Houston, H.J.Rozeboom, B.W.Dijkstra, R.G.Boot, J.M.Aerts, and D.M.van Aalten (2002).
Structure of human chitotriosidase. Implications for specific inhibitor design and function of mammalian chitinase-like lectins.
  J Biol Chem, 277, 25537-25544.
PDB codes: 1guv 1lg1 1lg2 1lq0
11821393 P.F.Varela, A.S.Llera, R.A.Mariuzza, and J.Tormo (2002).
Crystal structure of imaginal disc growth factor-2. A member of a new family of growth-promoting glycoproteins from Drosophila melanogaster.
  J Biol Chem, 277, 13229-13236.
PDB codes: 1jnd 1jne
11567159 A.A.Vagin, and M.N.Isupov (2001).
Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 57, 1451-1456.  
11481469 D.M.van Aalten, D.Komander, B.Synstad, S.Gåseidnes, M.G.Peter, and V.G.Eijsink (2001).
Structural insights into the catalytic mechanism of a family 18 exo-chitinase.
  Proc Natl Acad Sci U S A, 98, 8979-8984.
PDB codes: 1e6n 1e6p 1e6r 1e6z
11535590 Y.Wu, G.Egerton, A.P.Underwood, S.Sakuda, and A.E.Bianco (2001).
Expression and secretion of a larval-specific chitinase (family 18 glycosyl hydrolase) by the infective stages of the parasitic nematode, Onchocerca volvulus.
  J Biol Chem, 276, 42557-42564.  
10891067 C.A.Waddling, T.H.Plummer, A.L.Tarentino, and P.Van Roey (2000).
Structural basis for the substrate specificity of endo-beta-N-acetylglucosaminidase F(3).
  Biochemistry, 39, 7878-7885.
PDB codes: 1eok 1eom
10957628 M.Hahn, M.Hennig, B.Schlesier, and W.Höhne (2000).
Structure of jack bean chitinase.
  Acta Crystallogr D Biol Crystallogr, 56, 1096-1099.
PDB code: 1dxj
10545329 E.J.van Asselt, A.J.Dijkstra, K.H.Kalk, B.Takacs, W.Keck, and B.W.Dijkstra (1999).
Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand.
  Structure, 7, 1167-1180.
PDB codes: 1qus 1qut
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
  10595536 V.Rao, T.Cui, C.Guan, and P.Van Roey (1999).
Mutations of endo-beta-N-acetylglucosaminidase H active site residueAs sp130 anG glu132: activities and conformations.
  Protein Sci, 8, 2338-2346.
PDB codes: 1c3f 1c8x 1c8y 1c90 1c91 1c92 1c93
9761908 A.Vagin, and A.Teplyakov (1998).
A translation-function approach for heavy-atom location in macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 54, 400-402.  
9650272 R.Cohen-Kupiec, and I.Chet (1998).
The molecular biology of chitin digestion.
  Curr Opin Biotechnol, 9, 270-277.  
9748235 R.G.Boot, G.H.Renkema, M.Verhoek, A.Strijland, J.Bliek, T.M.de Meulemeester, M.M.Mannens, and J.M.Aerts (1998).
The human chitotriosidase gene. Nature of inherited enzyme deficiency.
  J Biol Chem, 273, 25680-25685.  
9692212 T.Yamagami, and M.Ishiguro (1998).
Complete amino acid sequences of chitinase-1 and -2 from bulbs of genus Tulipa.
  Biosci Biotechnol Biochem, 62, 1253-1257.  
9535180 M.Horsch, C.Mayer, U.Sennhauser, and D.M.Rast (1997).
Beta-N-acetylhexosaminidase: a target for the design of antifungal agents.
  Pharmacol Ther, 76, 187-218.  
8958090 C.E.Vorgias, A.Perrakis, and I.Tews (1996).
Structure-function studies on the chitinolytic enzymes of Serratia marcescens chitinase and chitobiase.
  Ann N Y Acad Sci, 799, 190-192.  
8673609 I.Tews, A.Perrakis, A.Oppenheim, Z.Dauter, K.S.Wilson, and C.E.Vorgias (1996).
Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease.
  Nat Struct Biol, 3, 638-648.
PDB codes: 1qba 1qbb 1qbc 1qbd
  8752320 T.Ohno, S.Armand, T.Hata, N.Nikaidou, B.Henrissat, M.Mitsutomi, and T.Watanabe (1996).
A modular family 19 chitinase found in the prokaryotic organism Streptomyces griseus HUT 6037.
  J Bacteriol, 178, 5065-5070.  
8535779 G.Davies, and B.Henrissat (1995).
Structures and mechanisms of glycosyl hydrolases.
  Structure, 3, 853-859.  
7704527 A.Perrakis, I.Tews, Z.Dauter, A.B.Oppenheim, I.Chet, K.S.Wilson, and C.E.Vorgias (1994).
Crystal structure of a bacterial chitinase at 2.3 A resolution.
  Structure, 2, 1169-1180.
PDB code: 1ctn
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.