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PDBsum entry 1chk
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Hydrolase (o-glycosyl)
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PDB id
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1chk
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.132
- chitosanase.
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Reaction:
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Endohydrolysis of beta-1,4-linkages between N-acetyl-D-glucosamine and D-glucosamine residues in a partly acetylated chitosan.
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Nat Struct Biol
3:155-162
(1996)
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PubMed id:
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X-ray structure of an anti-fungal chitosanase from streptomyces N174.
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E.M.Marcotte,
A.F.Monzingo,
S.R.Ernst,
R.Brzezinski,
J.D.Robertus.
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ABSTRACT
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We report the 2.4 A X-ray crystal structure of a protein with chitosan
endo-hydrolase activity isolated from Streptomyces N174. The structure was
solved using phases acquired by SIRAS from a two-site methyl mercury derivative
combined with solvent flattening and non-crystallographic two-fold symmetry
averaging, and refined to an R-factor of 18.5%. The mostly alpha-helical fold
reveals a structural core shared with several classes of lysozyme and barley
endochitinase, in spite of a lack of shared sequence. Based on this structural
similarity we postulate a putative active site, mechanism of action and mode of
substrate recognition. It appears that Glu 22 acts as an acid and Asp 40 serves
as a general base to activate a water molecule for an SN2 attack on the
glycosidic bond. A series of amino-acid side chains and backbone carbonyl groups
may bind the polycationic chitosan substrate in a deep electronegative binding
cleft.
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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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B.B.Aam,
E.B.Heggset,
A.L.Norberg,
M.Sørlie,
K.M.Vårum,
and
V.G.Eijsink
(2010).
Production of chitooligosaccharides and their potential applications in medicine.
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Mar Drugs,
8,
1482-1517.
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M.G.Johnsen,
O.C.Hansen,
and
P.Stougaard
(2010).
Isolation, characterization and heterologous expression of a novel chitosanase from Janthinobacterium sp. strain 4239.
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Microb Cell Fact,
9,
5.
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V.Gupta,
R.Prasanna,
C.Natarajan,
A.K.Srivastava,
and
J.Sharma
(2010).
Identification, characterization, and regulation of a novel antifungal chitosanase gene (cho) in Anabaena spp.
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Appl Environ Microbiol,
76,
2769-2777.
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J.Song,
H.Tan,
K.Mahmood,
R.H.Law,
A.M.Buckle,
G.I.Webb,
T.Akutsu,
and
J.C.Whisstock
(2009).
Prodepth: predict residue depth by support vector regression approach from protein sequences only.
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PLoS One,
4,
e7072.
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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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A.Ando,
A.Saito,
S.Arai,
S.Usuda,
M.Furuno,
N.Kaneko,
O.Shida,
and
Y.Nagata
(2008).
Molecular characterization of a novel family-46 chitosanase from Pseudomonas sp. A-01.
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Biosci Biotechnol Biochem,
72,
2074-2081.
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H.Hirakawa,
A.Ochi,
Y.Kawahara,
S.Kawamura,
T.Torikata,
and
S.Kuhara
(2008).
Catalytic Reaction Mechanism of Goose Egg-white Lysozyme by Molecular Modelling of Enzyme-Substrate Complex.
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J Biochem,
144,
753-761.
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S.Kawamura,
M.Ohkuma,
Y.Chijiiwa,
D.Kohno,
H.Nakagawa,
H.Hirakawa,
S.Kuhara,
and
T.Torikata
(2008).
Role of disulfide bonds in goose-type lysozyme.
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FEBS J,
275,
2818-2830.
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H.S.Lee,
J.S.Jang,
S.K.Choi,
D.W.Lee,
E.J.Kim,
H.C.Jung,
and
J.G.Pan
(2007).
Identification and expression of GH-8 family chitosanases from several Bacillus thuringiensis subspecies.
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FEMS Microbiol Lett,
277,
133-141.
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T.Goto,
Y.Abe,
Y.Kakuta,
K.Takeshita,
T.Imoto,
and
T.Ueda
(2007).
Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural basis of the catalytic mechanism and manifestation of its chitinase activity accompanied by quaternary structural change.
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J Biol Chem,
282,
27459-27467.
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PDB code:
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C.Yun,
D.Amakata,
Y.Matsuo,
H.Matsuda,
and
M.Kawamukai
(2005).
New chitosan-degrading strains that produce chitosanases similar to ChoA of Mitsuaria chitosanitabida.
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Appl Environ Microbiol,
71,
5138-5144.
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C.Blouin,
D.Butt,
and
A.J.Roger
(2004).
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
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Protein Sci,
13,
608-616.
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Y.Sakihama,
W.Adachi,
S.Shimizu,
T.Sunami,
T.Fukazawa,
M.Suzuki,
R.Yatsunami,
S.Nakamura,
and
A.Takénaka
(2004).
Crystallization and preliminary X-ray analyses of the active and the inactive forms of family GH-8 chitosanase with subclass II specificity from Bacillus sp. strain K17.
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Acta Crystallogr D Biol Crystallogr,
60,
2081-2083.
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T.Tanabe,
K.Morinaga,
T.Fukamizo,
and
M.Mitsutomi
(2003).
Novel chitosanase from Streptomyces griseus HUT 6037 with transglycosylation activity.
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Biosci Biotechnol Biochem,
67,
354-364.
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H.G.Yoon,
K.H.Lee,
H.Y.Kim,
H.K.Kim,
D.H.Shin,
B.S.Hong,
and
H.Y.Cho
(2002).
Gene cloning and biochemical analysis of thermostable chitosanase (TCH-2) from Bacillus coagulans CK108.
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Biosci Biotechnol Biochem,
66,
986-995.
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H.Kimoto,
H.Kusaoke,
I.Yamamoto,
Y.Fujii,
T.Onodera,
and
A.Taketo
(2002).
Biochemical and genetic properties of Paenibacillus glycosyl hydrolase having chitosanase activity and discoidin domain.
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J Biol Chem,
277,
14695-14702.
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C.P.Selitrennikoff
(2001).
Antifungal proteins.
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Appl Environ Microbiol,
67,
2883-2894.
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S.Thammasirirak,
T.Torikata,
K.Takami,
K.Murata,
and
T.Araki
(2001).
Purification and characterization of goose type lysozyme from cassowary (Casuarius casuarius) egg white.
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Biosci Biotechnol Biochem,
65,
584-592.
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H.D.Ly,
and
S.G.Withers
(1999).
Mutagenesis of glycosidases.
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Annu Rev Biochem,
68,
487-522.
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J.K.Park,
K.Shimono,
N.Ochiai,
K.Shigeru,
M.Kurita,
Y.Ohta,
K.Tanaka,
H.Matsuda,
and
M.Kawamukai
(1999).
Purification, characterization, and gene analysis of a chitosanase (ChoA) from Matsuebacter chitosanotabidus 3001.
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J Bacteriol,
181,
6642-6649.
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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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V.Nardi-Dei,
T.Kurihara,
C.Park,
M.Miyagi,
S.Tsunasawa,
K.Soda,
and
N.Esaki
(1999).
DL-2-Haloacid dehalogenase from Pseudomonas sp. 113 is a new class of dehalogenase catalyzing hydrolytic dehalogenation not involving enzyme-substrate ester intermediate.
|
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J Biol Chem,
274,
20977-20981.
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Y.Honda,
T.Fukamizo,
T.Okajima,
S.Goto,
I.Boucher,
and
R.Brzezinski
(1999).
Thermal unfolding of chitosanase from Streptomyces sp. N174: role of tryptophan residues in the protein structure stabilization.
|
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Biochim Biophys Acta,
1429,
365-376.
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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.J.Kirby
(1996).
Illuminating the ancient retainer.
|
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Nat Struct Biol,
3,
107-108.
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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
code is
shown on the right.
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Links
