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PDBsum entry 2baa
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Hydrolase (o-glycosyl)
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PDB id
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2baa
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.14
- chitinase.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.
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J Mol Biol
248:402-413
(1995)
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PubMed id:
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The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 A resolution.
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P.J.Hart,
H.D.Pfluger,
A.F.Monzingo,
T.Hollis,
J.D.Robertus.
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ABSTRACT
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Class II chitinases (EC 3.2.1.14) are plant defense proteins. They hydrolyze
chitin, an insoluble beta-1,4-linked polymer of N-acetylglucosamine (NAG), which
is a major cell-wall component of many fungal hyphae. We previously reported the
three-dimensional structure of the 26 kDa class II endochitinase from barley
seeds at 2.8 A resolution, determined using multiple isomorphous replacement
(MIR) methods. Here, we report the crystallographic refinement of this chitinase
structure against data to 1.8 A resolution using rounds of hand rebuilding
coupled with molecular dynamics (X-PLOR). The final model has an R-value of
18.1% for the 5.0 to 1.8 A data shell and 19.8% for the 10.0 to 1.8 A shell, and
root-mean-square deviations from standard bond lengths and angles of 0.017 A and
2.88 degrees, respectively. The 243 residue molecule has one beta-sheet, ten
alpha-helices and three disulfide bonds; 129 water molecules are included in the
final model. We show structural comparisons confirming that chitinase secondary
structure resembles lysozyme at the active site region. Based on substrate
binding to lysozyme, we have built a hypothetical model for the binding of a
hexasaccharide into the pronounced active site cleft of chitinase. This provides
the first view of likely substrate interactions from this family of enzymes; the
model is consistent with a lysozyme-like mechanism of action in which Glu67 acts
as proton donor and Glu89 is likely to stabilize the transition state
oxycarbonium ion. These binding site residues, and many hydrophobic residues are
conserved in a range of plant chitinases. This endochitinase structure will
serve as a model for other plant chitinases, and that catalytic models based on
this structure will be applicable to the entire enzyme family.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.J.Lai,
N.T.Lin,
A.Hu,
P.C.Soo,
L.K.Chen,
L.H.Chen,
and
K.C.Chang
(2011).
Antibacterial activity of Acinetobacter baumannii phage Ï•AB2 endolysin (LysAB2) against both gram-positive and gram-negative bacteria.
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Appl Microbiol Biotechnol,
90,
529-539.
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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).
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Glycobiology,
21,
644-654.
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C.Neeraja,
K.Anil,
P.Purushotham,
K.Suma,
P.Sarma,
B.M.Moerschbacher,
and
A.R.Podile
(2010).
Biotechnological approaches to develop bacterial chitinases as a bioshield against fungal diseases of plants.
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Crit Rev Biotechnol,
30,
231-241.
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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.
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FEBS J,
277,
2683-2695.
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PDB codes:
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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.
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Proteins,
78,
2295-2305.
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PDB code:
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D.N.Patil,
M.Datta,
A.Chaudhary,
S.Tomar,
A.K.Sharma,
and
P.Kumar
(2009).
Isolation, purification, crystallization and preliminary crystallographic studies of chitinase from tamarind (Tamarindus indica) seeds.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
343-345.
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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.
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FEBS J,
276,
857-869.
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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.
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Plant Mol Biol,
71,
277-289.
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PDB codes:
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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.
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FEBS J,
275,
2240-2254.
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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.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
371-374.
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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.
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BMC Biochem,
9,
2.
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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.
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FEBS J,
274,
3695-3703.
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PDB codes:
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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.
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Plant J,
49,
184-193.
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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.
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FEBS J,
273,
4889-4900.
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PDB code:
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K.E.Kabir,
D.Hirowatari,
K.Watanabe,
and
D.Koga
(2006).
Purification and characterization of a novel isozyme of chitinase from Bombyx mori.
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Biosci Biotechnol Biochem,
70,
252-262.
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N.Dahiya,
R.Tewari,
and
G.S.Hoondal
(2006).
Biotechnological aspects of chitinolytic enzymes: a review.
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Appl Microbiol Biotechnol,
71,
773-782.
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T.Kawase,
S.Yokokawa,
A.Saito,
T.Fujii,
N.Nikaidou,
K.Miyashita,
and
T.Watanabe
(2006).
Comparison of enzymatic and antifungal properties between family 18 and 19 chitinases from S. coelicolor A3(2).
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Biosci Biotechnol Biochem,
70,
988-998.
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J.Pei,
and
N.V.Grishin
(2005).
COG3926 and COG5526: a tale of two new lysozyme-like protein families.
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Protein Sci,
14,
2574-2581.
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V.Seidl,
B.Huemer,
B.Seiboth,
and
C.P.Kubicek
(2005).
A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases.
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FEBS J,
272,
5923-5939.
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C.M.Tang,
M.L.Chye,
S.Ramalingam,
S.W.Ouyang,
K.J.Zhao,
W.Ubhayasekera,
and
S.L.Mowbray
(2004).
Functional analyses of the chitin-binding domains and the catalytic domain of Brassica juncea chitinase BjCHI1.
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Plant Mol Biol,
56,
285-298.
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P.Tiffin
(2004).
Comparative evolutionary histories of chitinase genes in the Genus zea and Family poaceae.
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Genetics,
167,
1331-1340.
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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.
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Appl Environ Microbiol,
70,
1135-1144.
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T.Mitsunaga,
M.Iwase,
W.Ubhayasekera,
S.L.Mowbray,
and
D.Koga
(2004).
Molecular cloning of a genomic DNA encoding yam class IV chitinase.
|
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Biosci Biotechnol Biochem,
68,
1508-1517.
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M.Ueda,
M.Kojima,
T.Yoshikawa,
N.Mitsuda,
K.Araki,
T.Kawaguchi,
K.Miyatake,
M.Arai,
and
T.Fukamizo
(2003).
A novel type of family 19 chitinase from Aeromonas sp. No.10S-24. Cloning, sequence, expression, and the enzymatic properties.
|
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Eur J Biochem,
270,
2513-2520.
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N.H.Truong,
S.M.Park,
Y.Nishizawa,
T.Watanabe,
T.Sasaki,
and
Y.Itoh
(2003).
Structure, heterologous expression, and properties of rice (Oryza sativa L.) family 19 chitinases.
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Biosci Biotechnol Biochem,
67,
1063-1070.
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Y.Itoh,
K.Takahashi,
H.Takizawa,
N.Nikaidou,
H.Tanaka,
H.Nishihashi,
T.Watanabe,
and
Y.Nishizawa
(2003).
Family 19 chitinase of Streptomyces griseus HUT6037 increases plant resistance to the fungal disease.
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Biosci Biotechnol Biochem,
67,
847-855.
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Y.Itoh,
T.Kawase,
N.Nikaidou,
H.Fukada,
M.Mitsutomi,
T.Watanabe,
and
Y.Itoh
(2002).
Functional analysis of the chitin-binding domain of a family 19 chitinase from Streptomyces griseus HUT6037: substrate-binding affinity and cis-dominant increase of antifungal function.
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Biosci Biotechnol Biochem,
66,
1084-1092.
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J.G.Bishop,
A.M.Dean,
and
T.Mitchell-Olds
(2000).
Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution.
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Proc Natl Acad Sci U S A,
97,
5322-5327.
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M.Hahn,
M.Hennig,
B.Schlesier,
and
W.Höhne
(2000).
Structure of jack bean chitinase.
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Acta Crystallogr D Biol Crystallogr,
56,
1096-1099.
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PDB code:
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S.Cottaz,
B.Brasme,
and
H.Driguez
(2000).
A fluorescence-quenched chitopentaose for the study of endo-chitinases and chitobiosidases.
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Eur J Biochem,
267,
5593-5600.
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T.Hollis,
A.F.Monzingo,
K.Bortone,
S.Ernst,
R.Cox,
and
J.D.Robertus
(2000).
The X-ray structure of a chitinase from the pathogenic fungus Coccidioides immitis.
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Protein Sci,
9,
544-551.
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PDB code:
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T.Ikegami,
T.Okada,
M.Hashimoto,
S.Seino,
T.Watanabe,
and
M.Shirakawa
(2000).
Solution structure of the chitin-binding domain of Bacillus circulans WL-12 chitinase A1.
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J Biol Chem,
275,
13654-13661.
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PDB code:
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Y.Ponath,
H.Vollberg,
K.Hahlbrock,
and
E.Kombrink
(2000).
Two differentially regulated class II chitinases from parsley.
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Biol Chem,
381,
667-678.
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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.
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J Biol Chem,
274,
30818-30825.
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PDB code:
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J.D.Robertus,
A.F.Monzingo,
E.M.Marcotte,
and
P.J.Hart
(1998).
Structural analysis shows five glycohydrolase families diverged from a common ancestor.
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J Exp Zool,
282,
127-132.
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K.A.Brameld,
and
W.A.Goddard
(1998).
The role of enzyme distortion in the single displacement mechanism of family 19 chitinases.
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Proc Natl Acad Sci U S A,
95,
4276-4281.
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T.Yamagami,
and
G.Funatsu
(1998).
Identification of the aspartic acid residue located at or near substrate-binding site of rye seed chitinase-c.
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Biosci Biotechnol Biochem,
62,
383-385.
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A.V.Efimov
(1997).
Structural trees for protein superfamilies.
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Proteins,
28,
241-260.
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B.Henrissat,
and
G.Davies
(1997).
Structural and sequence-based classification of glycoside hydrolases.
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Curr Opin Struct Biol,
7,
637-644.
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A.F.Monzingo,
E.M.Marcotte,
P.J.Hart,
and
J.D.Robertus
(1996).
Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core.
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Nat Struct Biol,
3,
133-140.
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E.M.Marcotte,
A.F.Monzingo,
S.R.Ernst,
R.Brzezinski,
and
J.D.Robertus
(1996).
X-ray structure of an anti-fungal chitosanase from streptomyces N174.
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Nat Struct Biol,
3,
155-162.
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PDB code:
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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.
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Nat Struct Biol,
3,
638-648.
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PDB codes:
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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.
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J Bacteriol,
178,
5065-5070.
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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.
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Links
