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PDBsum entry 1ed7
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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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DOI no:
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J Biol Chem
275:13654-13661
(2000)
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PubMed id:
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Solution structure of the chitin-binding domain of Bacillus circulans WL-12 chitinase A1.
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T.Ikegami,
T.Okada,
M.Hashimoto,
S.Seino,
T.Watanabe,
M.Shirakawa.
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ABSTRACT
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The three-dimensional structure of the chitin-binding domain (ChBD) of chitinase
A1 (ChiA1) from a Gram-positive bacterium, Bacillus circulans WL-12, was
determined by means of multidimensional heteronuclear NMR methods. ChiA1 is a
glycosidase that hydrolyzes chitin and is composed of an N-terminal catalytic
domain, two fibronectin type III-like domains, and C-terminal ChBD(ChiA1) (45
residues, Ala(655)-Gln(699)), which binds specifically to insoluble chitin.
ChBD(ChiA1) has a compact and globular structure with the topology of a twisted
beta-sandwich. This domain contains two antiparallel beta-sheets, one composed
of three strands and the other of two strands. The core region formed by the
hydrophobic and aromatic residues makes the overall structure rigid and compact.
The overall topology of ChBD(ChiA1) is similar to that of the cellulose-binding
domain (CBD) of Erwinia chrysanthemi endoglucanase Z (CBD(EGZ)). However,
ChBD(ChiA1) lacks the three aromatic residues aligned linearly and exposed to
the solvent, which probably interact with cellulose in CBDs. Therefore, the
binding mechanism of a group of ChBDs including ChBD(ChiA1) may be different
from that proposed for CBDs.
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Selected figure(s)
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Figure 2.
Fig. 2. Summary of the structure information obtained in
the NMR experiments. A, summary of the sequential and medium
range NOE connectivities, secondary structures, chemical shift
indices, amide hydrogen exchange rates, 3J[HNH  ]coupling
constants, and solvent accessibility values for ChBD[ChiA1]. The
NOE connectivities are represented by bars, the size of which
indicates the NOE intensity (strong, medium, or weak). The
notation d[ N(i, i
+ 1)], for example, represents the connectivity between the  proton
resonance of a residue (i) and the amide proton resonance of the
subsequent residue (i + 1) in the sequence. Amide protons that
were exchanged slowly at pH 6.0 and 298 K are indicated. The
residues with life times of >0.5 h and <4 h are indicated by
open circles, >4 h and <18 h by half closed circles, and >18 h
by closed circles. The three-bond scalar coupling constants
between spins 1HN and 1H (3J[HNH
]) of
<4.9 Hz are indicated by open boxes, >4.9 Hz and <8.5 Hz by
one-third closed boxes, >8.5 Hz and <10.0 Hz by two-thirds
closed boxes, and >10.0 Hz by closed boxes. The chemical shift
indices (CSI) (38) are plotted for 1H resonances.
Upper bars, +1; lower bars,  1;
horizontal lines, 0. The solvent accessibility was calculated
with the program MOLMOL (36) for the side chain of each residue
and is shown by the bar height ranging from 0 to 60%. The figure
was produced with the program VINCE (Rowland Institute for
Science). B, the distance information defining the  -sheets of
ChBD[ChiA1]. The intra- and interstrand NOEs are indicated by
arrows. The hydrogen bonds used for the structure calculations
are indicated by dotted lines. The residues constituting the
-strands are
labeled with black boxes. C, schematic diagram of the -strands of
ChBD[ChiA1]. The diagram is drawn in the same direction as in B.
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Figure 6.
Fig. 6. The residues that may interact with chitin. The
side chain atoms of these residues are shown in a space-filling
model on a ribbon representation of ChBD[ChiA1] in stereo.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2000,
275,
13654-13661)
copyright 2000.
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Figures were
selected
by an automated process.
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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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C.Neeraja,
R.Subramanyam,
B.M.Moerschbacher,
and
A.R.Podile
(2010).
Swapping the chitin-binding domain in Bacillus chitinases improves the substrate binding affinity and conformational stability.
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Mol Biosyst,
6,
1492-1502.
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M.W.Delpin,
and
A.E.Goodman
(2009).
Nutrient regime regulates complex transcriptional start site usage within a Pseudoalteromonas chitinase gene cluster.
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ISME J,
3,
1053-1063.
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S.Kudan,
and
R.Pichyangkura
(2009).
Purification and characterization of thermostable chitinase from Bacillus licheniformis SK-1.
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Appl Biochem Biotechnol,
157,
23-35.
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B.Synstad,
G.Vaaje-Kolstad,
F.H.Cederkvist,
S.F.Saua,
S.J.Horn,
V.G.Eijsink,
and
M.Sørlie
(2008).
Expression and characterization of endochitinase C from Serratia marcescens BJL200 and its purification by a one-step general chitinase purification method.
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Biosci Biotechnol Biochem,
72,
715-723.
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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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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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H.H.Chuang,
and
F.P.Lin
(2007).
New role of C-terminal 30 amino acids on the insoluble chitin hydrolysis in actively engineered chitinase from Vibrio parahaemolyticus.
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Appl Microbiol Biotechnol,
76,
123-133.
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S.K.Park,
C.W.Kim,
H.Kim,
J.S.Jung,
and
G.E.Harman
(2007).
Cloning and high-level production of a chitinase from Chromobacterium sp. and the role of conserved or nonconserved residues on its catalytic activity.
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Appl Microbiol Biotechnol,
74,
791-804.
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F.H.Cederkvist,
A.D.Zamfir,
S.Bahrke,
V.G.Eijsink,
M.Sørlie,
J.Peter-Katalinić,
and
M.G.Peter
(2006).
Identification of a high-affinity-binding oligosaccharide by (+) nanoelectrospray quadrupole time-of-flight tandem mass spectrometry of a noncovalent enzyme-ligand complex.
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Angew Chem Int Ed Engl,
45,
2429-2434.
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S.DebRoy,
J.Dao,
M.Söderberg,
O.Rossier,
and
N.P.Cianciotto
(2006).
Legionella pneumophila type II secretome reveals unique exoproteins and a chitinase that promotes bacterial persistence in the lung.
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Proc Natl Acad Sci U S A,
103,
19146-19151.
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Y.Itoh,
J.Watanabe,
H.Fukada,
R.Mizuno,
Y.Kezuka,
T.Nonaka,
and
T.Watanabe
(2006).
Importance of Trp59 and Trp60 in chitin-binding, hydrolytic, and antifungal activities of Streptomyces griseus chitinase C.
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Appl Microbiol Biotechnol,
72,
1176-1184.
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A.Fokine,
P.G.Leiman,
M.M.Shneider,
B.Ahvazi,
K.M.Boeshans,
A.C.Steven,
L.W.Black,
V.V.Mesyanzhinov,
and
M.G.Rossmann
(2005).
Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry.
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Proc Natl Acad Sci U S A,
102,
7163-7168.
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PDB codes:
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F.Hoster,
J.E.Schmitz,
and
R.Daniel
(2005).
Enrichment of chitinolytic microorganisms: isolation and characterization of a chitinase exhibiting antifungal activity against phytopathogenic fungi from a novel Streptomyces strain.
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Appl Microbiol Biotechnol,
66,
434-442.
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P.A.Colussi,
C.A.Specht,
and
C.H.Taron
(2005).
Characterization of a nucleus-encoded chitinase from the yeast Kluyveromyces lactis.
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Appl Environ Microbiol,
71,
2862-2869.
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Q.Li,
F.Wang,
Y.Zhou,
and
X.Xiao
(2005).
Putative exposed aromatic and hydroxyl residues on the surface of the N-terminal domains of Chi1 from Aeromonas caviae CB101 are essential for chitin binding and hydrolysis.
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Appl Environ Microbiol,
71,
7559-7561.
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S.Züger,
and
H.Iwai
(2005).
Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies.
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Nat Biotechnol,
23,
736-740.
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Z.X.Lu,
A.Laroche,
and
H.C.Huang
(2005).
Isolation and characterization of chitinases from Verticillium lecanii.
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Can J Microbiol,
51,
1045-1055.
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T.Tenno,
K.Fujiwara,
H.Tochio,
K.Iwai,
E.H.Morita,
H.Hayashi,
S.Murata,
H.Hiroaki,
M.Sato,
K.Tanaka,
and
M.Shirakawa
(2004).
Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains.
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Genes Cells,
9,
865-875.
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F.P.Wang,
Q.Li,
Y.Zhou,
M.G.Li,
and
X.Xiao
(2003).
The C-terminal module of Chi1 from Aeromonas caviae CB101 has a function in substrate binding and hydrolysis.
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Proteins,
53,
908-916.
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D.Y.Kobayashi,
R.M.Reedy,
J.Bick,
and
P.V.Oudemans
(2002).
Characterization of a chitinase gene from Stenotrophomonas maltophilia strain 34S1 and its involvement in biological control.
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Appl Environ Microbiol,
68,
1047-1054.
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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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M.L.Wu,
Y.C.Chuang,
J.P.Chen,
C.S.Chen,
and
M.C.Chang
(2001).
Identification and characterization of the three chitin-binding domains within the multidomain chitinase Chi92 from Aeromonas hydrophila JP101.
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Appl Environ Microbiol,
67,
5100-5106.
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Y.Bourne,
and
B.Henrissat
(2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
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Curr Opin Struct Biol,
11,
593-600.
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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
