 |
PDBsum entry 1ffr
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.3.2.1.14
- chitinase.
|
|
|
|
|
|
|
Reaction:
|
|
Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
40:11338-11343
(2001)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
|
|
Y.Papanikolau,
G.Prag,
G.Tavlas,
C.E.Vorgias,
A.B.Oppenheim,
K.Petratos.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Chitinase A (ChiA) from the bacterium Serratia marcescens is a hydrolytic
enzyme, which cleaves beta-1,4-glycosidic bonds of the natural biopolymer chitin
to generate di-N-acetyl-chitobiose. The refined structure of ChiA at 1.55 A
shows that residue Asp313, which is located near the catalytic proton donor
residue Glu315, is found in two alternative conformations of equal occupancy. In
addition, the structures of the cocrystallized mutant proteins D313A, E315Q,
Y390F, and D391A with octa- or hexa-N-acetyl-glucosamine have been refined at
high resolution and the interactions with the substrate have been characterized.
The obtained results clearly show that the active site is a semiclosed tunnel.
Upon binding, the enzyme bends and rotates the substrate in the vicinity of the
scissile bond. Furthermore, the enzyme imposes a critical "chair" to "boat"
conformational change on the sugar residue bound to the -1 subsite. According to
our results, we suggest that residues Asp313 and Tyr390 along with Glu315 play a
central role in the catalysis. We propose that after the protonation of the
substrate glycosidic bond, Asp313 that interacts with Asp311 flips to its
alternative position where it interacts with Glu315 thus forcing the substrate
acetamido group of -1 sugar to rotate around the C2-N2 bond. As a result of
these structural changes, the water molecule that is hydrogen-bonded to Tyr390
and the NH of the acetamido group is displaced to a position that allows the
completion of hydrolysis. The presented results suggest a mechanism for ChiA
that modifies the earlier proposed "substrate assisted" catalysis.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
E.A.Vasconcelos,
C.G.Santana,
C.V.Godoy,
C.D.Seixas,
M.S.Silva,
L.R.Moreira,
O.B.Oliveira-Neto,
D.Price,
E.Fitches,
E.X.Filho,
A.Mehta,
J.A.Gatehouse,
and
M.F.Grossi-De-Sa
(2011).
A new chitinase-like xylanase inhibitor protein (XIP) from coffee (Coffea arabica) affects Soybean Asian rust (Phakopsora pachyrhizi) spore germination.
|
| |
BMC Biotechnol,
11,
14.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
H.Zakariassen,
B.B.Aam,
S.J.Horn,
K.M.Vårum,
M.Sørlie,
and
V.G.Eijsink
(2009).
Aromatic Residues in the Catalytic Center of Chitinase A from Serratia marcescens Affect Processivity, Enzyme Activity, and Biomass Converting Efficiency.
|
| |
J Biol Chem,
284,
10610-10617.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
| |
Biosci Biotechnol Biochem,
72,
715-723.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
E.Stefanidi,
and
C.E.Vorgias
(2008).
Molecular analysis of the gene encoding a new chitinase from the marine psychrophilic bacterium Moritella marina and biochemical characterization of the recombinant enzyme.
|
| |
Extremophiles,
12,
541-552.
|
|
|
|
|
|
|
M.Lian,
S.Lin,
and
R.Zeng
(2007).
Chitinase gene diversity at a deep sea station of the east Pacific nodule province.
|
| |
Extremophiles,
11,
463-467.
|
|
|
|
|
|
|
M.Ohmae,
K.Sakaguchi,
T.Kaneto,
S.Fujikawa,
and
S.Kobayashi
(2007).
Keratanase II-catalyzed synthesis of keratan sulfate oligomers by using sugar oxazolines as transition-state analogue substrate monomers: a novel insight into the enzymatic catalysis mechanism.
|
| |
Chembiochem,
8,
1710-1720.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
| |
Appl Microbiol Biotechnol,
74,
791-804.
|
|
|
|
|
|
|
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.
|
| |
Angew Chem Int Ed Engl,
45,
2429-2434.
|
|
|
|
|
|
|
H.Bach,
and
D.L.Gutnick
(2006).
Novel polysaccharide-protein-based amphipathic formulations.
|
| |
Appl Microbiol Biotechnol,
71,
34-38.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
G.R.LeCleir,
A.Buchan,
and
J.T.Hollibaugh
(2004).
Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions.
|
| |
Appl Environ Microbiol,
70,
6977-6983.
|
|
|
|
|
|
|
M.Hrmova,
R.De Gori,
B.J.Smith,
A.Vasella,
J.N.Varghese,
and
G.B.Fincher
(2004).
Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
|
| |
J Biol Chem,
279,
4970-4980.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.Matsui,
T.Kumasaka,
K.Endo,
T.Sato,
S.Nakamura,
and
N.Tanaka
(2004).
Crystallization and preliminary X-ray crystallographic analysis of chitinase F1 (ChiF1) from the alkaliphilic Nocardiopsis sp. strain F96.
|
| |
Acta Crystallogr D Biol Crystallogr,
60,
2016-2018.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
A.Vasella,
G.J.Davies,
and
M.Böhm
(2002).
Glycosidase mechanisms.
|
| |
Curr Opin Chem Biol,
6,
619-629.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
S.J.Williams,
B.L.Mark,
D.J.Vocadlo,
M.N.James,
and
S.G.Withers
(2002).
Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state.
|
| |
J Biol Chem,
277,
40055-40065.
|
|
|
PDB codes:
|
|
|
|
|
|
|
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.
|
|
Links
