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PDBsum entry 1ayh
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DOI no:
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Proc Natl Acad Sci U S A
90:5287-5291
(1993)
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PubMed id:
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Molecular and active-site structure of a Bacillus 1,3-1,4-beta-glucanase.
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T.Keitel,
O.Simon,
R.Borriss,
U.Heinemann.
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ABSTRACT
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The three-dimensional structure of the hybrid Bacillus 1,3-1,4-beta-glucanase
(beta-glucanase; 1,3-1,4-beta-D-glucan 4-glucanohydrolase, lichenase, EC
3.2.1.73) designated H(A16-M) was determined by x-ray crystallography at a
resolution of 2.0 A and refined to an R value of 16.4% using stereochemical
restraints. The protein molecule consists mainly of two seven-stranded
antiparallel beta-pleated sheets arranged atop each other to form a compact,
sandwich-like structure. A channel crossing one side of the protein molecule
accommodates an inhibitor, 3,4-epoxybutyl beta-D-cellobioside, which binds
covalently to the side chain of Glu-105, as seen in a crystal structure analysis
at 2.8-A resolution of the protein-inhibitor complex (R = 16.8%). That Glu-105
may be indispensible for enzyme catalysis by H(A16-M) is suggested by
site-directed mutagenesis of this residue, which inevitably leads to an inactive
enzyme.
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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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A.P.Yeh,
P.Abdubek,
T.Astakhova,
H.L.Axelrod,
C.Bakolitsa,
X.Cai,
D.Carlton,
C.Chen,
H.J.Chiu,
M.Chiu,
T.Clayton,
D.Das,
M.C.Deller,
L.Duan,
K.Ellrott,
C.L.Farr,
J.Feuerhelm,
J.C.Grant,
A.Grzechnik,
G.W.Han,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
P.Kozbial,
S.S.Krishna,
A.Kumar,
W.W.Lam,
D.Marciano,
D.McMullan,
M.D.Miller,
A.T.Morse,
E.Nigoghossian,
A.Nopakun,
L.Okach,
C.Puckett,
R.Reyes,
H.J.Tien,
C.B.Trame,
H.van den Bedem,
D.Weekes,
T.Wooten,
Q.Xu,
K.O.Hodgson,
J.Wooley,
M.A.Elsliger,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2010).
Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Šresolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
66,
1287-1296.
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PDB code:
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J.H.Chen,
L.C.Tsai,
H.C.Huang,
and
L.F.Shyur
(2010).
Structural and catalytic roles of amino acid residues located at substrate-binding pocket in Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase.
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Proteins,
78,
2820-2830.
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M.S.Bulmer,
I.Bachelet,
R.Raman,
R.B.Rosengaus,
and
R.Sasisekharan
(2009).
Targeting an antimicrobial effector function in insect immunity as a pest control strategy.
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Proc Natl Acad Sci U S A,
106,
12652-12657.
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L.C.Tsai,
H.C.Huang,
C.H.Hsiao,
Y.N.Chiang,
L.F.Shyur,
Y.S.Lin,
and
S.H.Lee
(2008).
Mutational and structural studies of the active-site residues in truncated Fibrobacter succinogenes1,3-1,4-beta-D-glucanase.
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Acta Crystallogr D Biol Crystallogr,
64,
1259-1266.
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L.C.Tsai,
Y.N.Chen,
and
L.F.Shyur
(2008).
Structural modeling of glucanase-substrate complexes suggests a conserved tyrosine is involved in carbohydrate recognition in plant 1,3-1,4-beta-D-glucanases.
|
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J Comput Aided Mol Des,
22,
915-923.
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S.Yang,
Y.Wang,
Z.Jiang,
and
C.Hua
(2008).
Crystallization and preliminary X-ray analysis of a 1,3-1,4-beta-glucanase from Paecilomyces thermophila.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
754-756.
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T.Y.Zakharian,
L.Di Costanzo,
and
D.W.Christianson
(2008).
Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I.
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Org Biomol Chem,
6,
3240-3243.
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PDB code:
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A.Abyzov,
and
V.A.Ilyin
(2007).
A comprehensive analysis of non-sequential alignments between all protein structures.
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BMC Struct Biol,
7,
78.
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D.von Wettstein
(2007).
From analysis of mutants to genetic engineering.
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Annu Rev Plant Biol,
58,
1.
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G.Fibriansah,
S.Masuda,
N.Koizumi,
S.Nakamura,
and
T.Kumasaka
(2007).
The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.
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Proteins,
69,
683-690.
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PDB code:
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G.Michel,
P.Nyval-Collen,
T.Barbeyron,
M.Czjzek,
and
W.Helbert
(2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.
|
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Appl Microbiol Biotechnol,
71,
23-33.
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J.Vasur,
R.Kawai,
A.M.Larsson,
K.Igarashi,
M.Sandgren,
M.Samejima,
and
J.Ståhlberg
(2006).
X-ray crystallographic native sulfur SAD structure determination of laminarinase Lam16A from Phanerochaete chrysosporium.
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Acta Crystallogr D Biol Crystallogr,
62,
1422-1429.
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PDB code:
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J.Jänis,
J.Hakanpää,
N.Hakulinen,
F.M.Ibatullin,
A.Hoxha,
P.J.Derrick,
J.Rouvinen,
and
P.Vainiotalo
(2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
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FEBS J,
272,
2317-2333.
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PDB code:
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W.Tempel,
Z.J.Liu,
P.S.Horanyi,
L.Deng,
D.Lee,
M.G.Newton,
J.P.Rose,
H.Ashida,
S.C.Li,
Y.T.Li,
and
B.C.Wang
(2005).
Three-dimensional structure of GlcNAcalpha1-4Gal releasing endo-beta-galactosidase from Clostridium perfringens.
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Proteins,
59,
141-144.
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PDB code:
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Z.Pang,
Y.N.Kang,
M.Ban,
M.Oda,
R.Kobayashi,
M.Ohnishi,
and
B.Mikami
(2005).
Crystallization and preliminary crystallographic analysis of endo-1,3-beta-glucanase from Arthrobacter sp.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
68-70.
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J.Allouch,
W.Helbert,
B.Henrissat,
and
M.Czjzek
(2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
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Structure,
12,
623-632.
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PDB code:
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M.Strohmeier,
M.Hrmova,
M.Fischer,
A.J.Harvey,
G.B.Fincher,
and
J.Pleiss
(2004).
Molecular modeling of family GH16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae.
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Protein Sci,
13,
3200-3213.
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J.D.Schrag,
D.O.Procopio,
M.Cygler,
D.Y.Thomas,
and
J.J.Bergeron
(2003).
Lectin control of protein folding and sorting in the secretory pathway.
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Trends Biochem Sci,
28,
49-57.
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M.Muraki,
and
K.Harata
(2003).
X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine.
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J Mol Recognit,
16,
72-82.
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PDB codes:
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N.Miyanishi,
Y.Matsubara,
N.Hamada,
T.Kobayashi,
C.Imada,
and
E.Watanabe
(2003).
The action modes of an extracellular beta-1,3-glucanase isolated from Bacillus clausii NM-1 on beta-1,3-glucooligosaccharides.
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J Biosci Bioeng,
96,
32-37.
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H.Ashida,
K.Maskos,
S.C.Li,
and
Y.T.Li
(2002).
Characterization of a novel endo-beta-galactosidase specific for releasing the disaccharide GlcNAc alpha 1-->4Gal from glycoconjugates.
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Biochemistry,
41,
2388-2395.
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M.Abou-Hachem,
E.N.Karlsson,
P.J.Simpson,
S.Linse,
P.Sellers,
M.P.Williamson,
S.J.Jamieson,
H.J.Gilbert,
D.N.Bolam,
and
O.Holst
(2002).
Calcium binding and thermostability of carbohydrate binding module CBM4-2 of Xyn10A from Rhodothermus marinus.
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Biochemistry,
41,
5720-5729.
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G.Michel,
L.Chantalat,
E.Duee,
T.Barbeyron,
B.Henrissat,
B.Kloareg,
and
O.Dideberg
(2001).
The kappa-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases.
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Structure,
9,
513-525.
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PDB code:
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G.Rudenko,
E.Hohenester,
and
Y.A.Muller
(2001).
LG/LNS domains: multiple functions -- one business end?
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Trends Biochem Sci,
26,
363-368.
|
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L.C.Tsai,
L.F.Shyur,
S.S.Lin,
and
H.S.Yuan
(2001).
Crystallization and preliminary X-ray diffraction analysis of the 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes.
|
| |
Acta Crystallogr D Biol Crystallogr,
57,
1303-1306.
|
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A.A.McCarthy,
D.D.Morris,
P.L.Bergquist,
and
E.N.Baker
(2000).
Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.
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Acta Crystallogr D Biol Crystallogr,
56,
1367-1375.
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PDB code:
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A.Planas
(2000).
Bacterial 1,3-1,4-beta-glucanases: structure, function and protein engineering.
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| |
Biochim Biophys Acta,
1543,
361-382.
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F.Lipari,
and
A.Herscovics
(1999).
Calcium binding to the class I alpha-1,2-mannosidase from Saccharomyces cerevisiae occurs outside the EF hand motif.
|
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Biochemistry,
38,
1111-1118.
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G.Michel,
T.Barbeyron,
D.Flament,
T.Vernet,
B.Kloareg,
and
O.Dideberg
(1999).
Expression, purification, crystallization and preliminary x-ray analysis of the kappa-carrageenase from Pseudoalteromonas carrageenovora.
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Acta Crystallogr D Biol Crystallogr,
55,
918-920.
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G.Rudenko,
T.Nguyen,
Y.Chelliah,
T.C.Südhof,
and
J.Deisenhofer
(1999).
The structure of the ligand-binding domain of neurexin Ibeta: regulation of LNS domain function by alternative splicing.
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Cell,
99,
93.
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PDB code:
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K.Piotukh,
V.Serra,
R.Borriss,
and
A.Planas
(1999).
Protein-carbohydrate interactions defining substrate specificity in Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases as dissected by mutational analysis.
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Biochemistry,
38,
16092-16104.
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L.E.Driskill,
M.W.Bauer,
and
R.M.Kelly
(1999).
Synergistic interactions among beta-laminarinase, beta-1,4-glucanase, and beta-glucosidase from the hyperthermophilic archaeon Pyrococcus furiosus during hydrolysis of beta-1,4-, beta-1,3-, and mixed-linked polysaccharides.
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Biotechnol Bioeng,
66,
51-60.
|
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M.Muraki,
K.Harata,
N.Sugita,
and
K.Sato
(1999).
Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand.
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Biochemistry,
38,
540-548.
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PDB code:
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P.Campbell,
J.Braam,
and
L.V.McIntire
(1999).
In vitro activities of four xyloglucan endotransglycosylases from Arabidopsis.
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Plant J,
18,
371-382.
|
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R.C.Montijn,
E.Vink,
W.H.Müller,
A.J.Verkleij,
H.Van Den Ende,
B.Henrissat,
and
F.M.Klis
(1999).
Localization of synthesis of beta1,6-glucan in Saccharomyces cerevisiae.
|
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J Bacteriol,
181,
7414-7420.
|
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J.Aÿ,
F.Götz,
R.Borriss,
and
U.Heinemann
(1998).
Structure and function of the Bacillus hybrid enzyme GluXyn-1: native-like jellyroll fold preserved after insertion of autonomous globular domain.
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Proc Natl Acad Sci U S A,
95,
6613-6618.
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PDB code:
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J.Aÿ,
M.Hahn,
K.Decanniere,
K.Piotukh,
R.Borriss,
and
U.Heinemann
(1998).
Crystal structures and properties of de novo circularly permuted 1,3-1,4-beta-glucanases.
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Proteins,
30,
155-167.
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PDB codes:
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J.L.Viladot,
E.de Ramon,
O.Durany,
and
A.Planas
(1998).
Probing the mechanism of Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases by chemical rescue of inactive mutants at catalytically essential residues.
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Biochemistry,
37,
11332-11342.
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J.M.Görlach,
E.Van Der Knaap,
and
J.D.Walton
(1998).
Cloning and targeted disruption of MLG1, a gene encoding two of three extracellular mixed-linked glucanases of Cochliobolus carbonum.
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Appl Environ Microbiol,
64,
385-391.
|
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K.Gruber,
G.Klintschar,
M.Hayn,
A.Schlacher,
W.Steiner,
and
C.Kratky
(1998).
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
|
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Biochemistry,
37,
13475-13485.
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PDB code:
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P.Campbell,
J.Braam,
and
L.V.McIntire
(1998).
Co- and/or post-translational modifications are critical for TCH4 XET activity.
|
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Plant J,
15,
553-561.
|
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P.E.Johnson,
A.L.Creagh,
E.Brun,
K.Joe,
P.Tomme,
C.A.Haynes,
and
L.P.McIntosh
(1998).
Calcium binding by the N-terminal cellulose-binding domain from Cellulomonas fimi beta-1,4-glucanase CenC.
|
| |
Biochemistry,
37,
12772-12781.
|
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A.White,
and
D.R.Rose
(1997).
Mechanism of catalysis by retaining beta-glycosyl hydrolases.
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| |
Curr Opin Struct Biol,
7,
645-651.
|
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C.Malet,
and
A.Planas
(1997).
Mechanism of Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases: kinetics and pH studies with 4-methylumbelliferyl beta-D-glucan oligosaccharides.
|
| |
Biochemistry,
36,
13838-13848.
|
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G.Sulzenbacher,
M.Schülein,
and
G.J.Davies
(1997).
Structure of the endoglucanase I from Fusarium oxysporum: native, cellobiose, and 3,4-epoxybutyl beta-D-cellobioside-inhibited forms, at 2.3 A resolution.
|
| |
Biochemistry,
36,
5902-5911.
|
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PDB codes:
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L.F.Mackenzie,
G.J.Davies,
M.Schülein,
and
S.G.Withers
(1997).
Identification of the catalytic nucleophile of endoglucanase I from Fusarium oxysporum by mass spectrometry.
|
| |
Biochemistry,
36,
5893-5901.
|
 |
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|
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Y.Lindqvist,
and
G.Schneider
(1997).
Circular permutations of natural protein sequences: structural evidence.
|
| |
Curr Opin Struct Biol,
7,
422-427.
|
 |
|
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|
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A.White,
D.Tull,
K.Johns,
S.G.Withers,
and
D.R.Rose
(1996).
Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.
|
| |
Nat Struct Biol,
3,
149-154.
|
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PDB code:
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E.S.Bachman,
and
D.R.McClay
(1996).
Molecular cloning of the first metazoan beta-1,3 glucanase from eggs of the sea urchin Strongylocentrotus purpuratus.
|
| |
Proc Natl Acad Sci U S A,
93,
6808-6813.
|
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|
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G.Sulzenbacher,
H.Driguez,
B.Henrissat,
M.Schülein,
and
G.J.Davies
(1996).
Structure of the Fusarium oxysporum endoglucanase I with a nonhydrolyzable substrate analogue: substrate distortion gives rise to the preferred axial orientation for the leaving group.
|
| |
Biochemistry,
35,
15280-15287.
|
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PDB code:
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K.Welfle,
R.Misselwitz,
O.Politz,
R.Borriss,
and
H.Welfle
(1996).
Individual amino acids in the N-terminal loop region determine the thermostability and unfolding characteristics of bacterial glucanases.
|
| |
Protein Sci,
5,
2255-2265.
|
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|
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L.G.Jensen,
O.Olsen,
O.Kops,
N.Wolf,
K.K.Thomsen,
and
D.von Wettstein
(1996).
Transgenic barley expressing a protein-engineered, thermostable (1,3-1,4)-beta-glucanase during germination.
|
| |
Proc Natl Acad Sci U S A,
93,
3487-3491.
|
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|
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|
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M.Muraki,
K.Harata,
N.Sugita,
and
K.Sato
(1996).
Origin of carbohydrate recognition specificity of human lysozyme revealed by affinity labeling.
|
| |
Biochemistry,
35,
13562-13567.
|
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PDB codes:
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O.Olsen,
K.K.Thomsen,
J.Weber,
J.O.Duus,
I.Svendsen,
C.Wegener,
and
D.von Wettstein
(1996).
Transplanting two unique beta-glucanase catalytic activities into one multienzyme, which forms glucose.
|
| |
Biotechnology (N Y),
14,
71-76.
|
 |
|
|
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|
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P.E.Johnson,
M.D.Joshi,
P.Tomme,
D.G.Kilburn,
and
L.P.McIntosh
(1996).
Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy.
|
| |
Biochemistry,
35,
14381-14394.
|
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|
PDB codes:
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 |
R.Havukainen,
A.Törrönen,
T.Laitinen,
and
J.Rouvinen
(1996).
Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.
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| |
Biochemistry,
35,
9617-9624.
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 |
|
PDB codes:
|
 |
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|
 |
D.D.Leonidas,
B.L.Elbert,
Z.Zhou,
H.Leffler,
S.J.Ackerman,
and
K.R.Acharya
(1995).
Crystal structure of human Charcot-Leyden crystal protein, an eosinophil lysophospholipase, identifies it as a new member of the carbohydrate-binding family of galectins.
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| |
Structure,
3,
1379-1393.
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|
PDB code:
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|
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G.Davies,
and
B.Henrissat
(1995).
Structures and mechanisms of glycosyl hydrolases.
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Structure,
3,
853-859.
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J.de la Cruz,
J.A.Pintor-Toro,
T.Benítez,
A.Llobell,
and
L.C.Romero
(1995).
A novel endo-beta-1,3-glucanase, BGN13.1, involved in the mycoparasitism of Trichoderma harzianum.
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| |
J Bacteriol,
177,
6937-6945.
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K.Welfle,
R.Misselwitz,
H.Welfle,
O.Politz,
and
R.Borriss
(1995).
Influence of Ca2+ on conformation and stability of three bacterial hybrid glucanases.
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Eur J Biochem,
229,
726-735.
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M.Hahn,
T.Keitel,
and
U.Heinemann
(1995).
Crystal and molecular structure at 0.16-nm resolution of the hybrid Bacillus endo-1,3-1,4-beta-D-glucan 4-glucanohydrolase H(A16-M).
|
| |
Eur J Biochem,
232,
849-858.
|
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PDB code:
|
 |
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|
|
|
|
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M.Meldgaard,
J.Harthill,
B.Petersen,
and
O.Olsen
(1995).
Glycan modification of a thermostable recombinant (1-3, 1-4)-beta-glucanase secreted from Saccharomyces cerevisiae is determined by strain and culture conditions.
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Glycoconj J,
12,
380-390.
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M.Menéndez,
M.Gasset,
J.Laynez,
C.López-Zumel,
P.Usobiaga,
E.Töpfer-Petersen,
and
J.J.Calvete
(1995).
Analysis of the structural organization and thermal stability of two spermadhesins. Calorimetric, circular dichroic and Fourier-transform infrared spectroscopic studies.
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| |
Eur J Biochem,
234,
887-896.
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A.Törrönen,
A.Harkki,
and
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(1994).
Three-dimensional structure of endo-1,4-beta-xylanase II from Trichoderma reesei: two conformational states in the active site.
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EMBO J,
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2493-2501.
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G.E.Norris,
T.J.Stillman,
B.F.Anderson,
and
E.N.Baker
(1994).
The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.
|
| |
Structure,
2,
1049-1059.
|
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|
PDB code:
|
 |
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|
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J.N.Varghese,
T.P.Garrett,
P.M.Colman,
L.Chen,
P.B.Høj,
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(1994).
Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities.
|
| |
Proc Natl Acad Sci U S A,
91,
2785-2789.
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PDB codes:
|
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|
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L.Holm,
and
C.Sander
(1994).
Searching protein structure databases has come of age.
|
| |
Proteins,
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165-173.
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|
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M.Hahn,
K.Piotukh,
R.Borriss,
and
U.Heinemann
(1994).
Native-like in vivo folding of a circularly permuted jellyroll protein shown by crystal structure analysis.
|
| |
Proc Natl Acad Sci U S A,
91,
10417-10421.
|
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|
PDB codes:
|
 |
|
|
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|
 |
N.Srinivasan,
H.E.White,
J.Emsley,
S.P.Wood,
M.B.Pepys,
and
T.L.Blundell
(1994).
Comparative analyses of pentraxins: implications for protomer assembly and ligand binding.
|
| |
Structure,
2,
1017-1027.
|
 |
|
PDB codes:
|
 |
|
|
|
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|
 |
R.Dominguez,
H.Souchon,
and
P.M.Alzari
(1994).
Characterization of two crystal forms of Clostridium thermocellum endoglucanase CelC.
|
| |
Proteins,
19,
158-160.
|
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|
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|
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R.Spilliaert,
G.O.Hreggvidsson,
J.K.Kristjansson,
G.Eggertsson,
and
A.Palsdottir
(1994).
Cloning and sequencing of a Rhodothermus marinus gene, bglA, coding for a thermostable beta-glucanase and its expression in Escherichia coli.
|
| |
Eur J Biochem,
224,
923-930.
|
 |
|
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|
|
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S.D.Rufino,
and
T.L.Blundell
(1994).
Structure-based identification and clustering of protein families and superfamilies.
|
| |
J Comput Aided Mol Des,
8,
5.
|
 |
|
|
|
|
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T.Keitel,
M.Meldgaard,
and
U.Heinemann
(1994).
Cation binding to a Bacillus (1,3-1,4)-beta-glucanase. Geometry, affinity and effect on protein stability.
|
| |
Eur J Biochem,
222,
203-214.
|
 |
|
PDB code:
|
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|
|
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|
 |
O.Politz,
O.Simon,
O.Olsen,
and
R.Borriss
(1993).
Determinants for the enhanced thermostability of hybrid (1-3,1-4)-beta-glucanases.
|
| |
Eur J Biochem,
216,
829-834.
|
 |
|
 |
 |
|
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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}
}
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