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PDBsum entry 1h4h
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Glycoside hydrolase
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PDB id
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1h4h
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Contents |
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* Residue conservation analysis
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PDB id:
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Glycoside hydrolase
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Title:
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Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5b conformations at the active-centre
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Structure:
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Xylanase. Chain: a, b, c, d. Fragment: family 11 xylanase catalytic domain. Engineered: yes. Mutation: yes. Other_details: xylotriose in the active site
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Source:
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Bacillus agaradhaerens. Organism_taxid: 76935. Expressed in: bacillus licheniformis. Expression_system_taxid: 1402
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Resolution:
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1.90Å
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R-factor:
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0.184
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R-free:
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0.241
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Authors:
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E.Sabini,K.S.Wilson,S.Danielsen,M.Schulein,G.J.Davies
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Key ref:
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E.Sabini
et al.
(1999).
Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
Chem Biol,
6,
483-492.
PubMed id:
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Date:
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11-May-01
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Release date:
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09-May-02
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PROCHECK
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Headers
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References
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Q7SIE2
(Q7SIE2_SALAG) -
Endo-1,4-beta-xylanase from Salipaludibacillus agaradhaerens
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Seq:
Struc:
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209 a.a.
207 a.a.*
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Key: |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class:
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E.C.3.2.1.8
- endo-1,4-beta-xylanase.
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Reaction:
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Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
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Chem Biol
6:483-492
(1999)
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PubMed id:
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Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
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E.Sabini,
G.Sulzenbacher,
M.Dauter,
Z.Dauter,
P.L.Jørgensen,
M.Schülein,
C.Dupont,
G.J.Davies,
K.S.Wilson.
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ABSTRACT
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BACKGROUND: The enzymatic hydrolysis of glycosides involves the formation and
subsequent breakdown of a covalent glycosyl-enzyme intermediate via
oxocarbenium-ion-like transition states. The covalent intermediate may be
trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details
of the intermediate conformation and noncovalent interactions between enzyme and
oligosaccharide. Xylanases are important in industrial applications - in the
pulp and paper industry, pretreating wood with xylanases decreases the amount of
chlorine-containing chemicals used. Xylanases are structurally similar to
cellulases but differ in their specificity for xylose-based, versus
glucose-based, substrates. RESULTS: The structure of the family 11 xylanase,
Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography
in both native and xylobiosyl-enzyme intermediate forms at 1.78 A and 2.0 A
resolution, respectively. The covalent glycosyl-enzyme intermediate has been
trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike
covalent intermediate structures for glycoside hydrolases from other families,
the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual 2,5B
conformation. CONCLUSIONS: The 2,5B conformation found for the alpha-linked
xylobiosyl-enzyme intermediate of Xyl11, unlike the 4C1 chair conformation
observed for other systems, is consistent with the stereochemical constraints
required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11
covalent glycosyl-enzyme intermediate with the equivalent structure for the
related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the
likely determinants for substrate specificity in this clan of glycoside
hydrolases.
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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.Pollet,
J.A.Delcour,
and
C.M.Courtin
(2010).
Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families.
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Crit Rev Biotechnol,
30,
176-191.
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D.R.Carrillo,
C.Parthier,
N.Jänckel,
J.Grandke,
M.Stelter,
S.Schilling,
M.Boehme,
P.Neumann,
R.Wolf,
H.U.Demuth,
M.T.Stubbs,
and
J.U.Rahfeld
(2010).
Kinetic and structural characterization of bacterial glutaminyl cyclases from Zymomonas mobilis and Myxococcus xanthus.
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Biol Chem,
391,
1419-1428.
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PDB codes:
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J.M.Schmidt,
M.J.Howard,
M.Maestre-Martínez,
C.S.Pérez,
and
F.Löhr
(2009).
Variation in protein C(alpha)-related one-bond J couplings.
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Magn Reson Chem,
47,
16-30.
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P.Jommuengbout,
S.Pinitglang,
K.L.Kyu,
and
K.Ratanakhanokchai
(2009).
Substrate-binding site of family 11 xylanase from Bacillus firmus K-1 by molecular docking.
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Biosci Biotechnol Biochem,
73,
833-839.
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R.Carapito,
A.Imberty,
J.M.Jeltsch,
S.C.Byrns,
P.H.Tam,
T.L.Lowary,
A.Varrot,
and
V.Phalip
(2009).
Molecular Basis of Arabinobio-hydrolase Activity in Phytopathogenic Fungi: CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF FUSARIUM GRAMINEARUM GH93 EXO-{alpha}-L-ARABINANASE.
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J Biol Chem,
284,
12285-12296.
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PDB codes:
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Q.Wang,
and
T.Xia
(2008).
Enhancement of the activity and alkaline pH stability of Thermobifida fusca xylanase A by directed evolution.
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Biotechnol Lett,
30,
937-944.
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F.Löhr,
R.Hänsel,
V.V.Rogov,
and
V.Dötsch
(2007).
Improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins.
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J Biomol NMR,
37,
205-224.
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M.Kozak
(2006).
Solution scattering studies of conformation stability of xylanase XYNII from Trichoderma longibrachiatum.
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Biopolymers,
83,
95.
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N.Watanabe,
T.Akiba,
R.Kanai,
and
K.Harata
(2006).
Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.
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Acta Crystallogr D Biol Crystallogr,
62,
784-792.
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PDB codes:
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V.A.Money,
N.L.Smith,
A.Scaffidi,
R.V.Stick,
H.J.Gilbert,
and
G.J.Davies
(2006).
Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
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Angew Chem Int Ed Engl,
45,
5136-5140.
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PDB codes:
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E.J.Taylor,
A.Goyal,
C.I.Guerreiro,
J.A.Prates,
V.A.Money,
N.Ferry,
C.Morland,
A.Planas,
J.A.Macdonald,
R.V.Stick,
H.J.Gilbert,
C.M.Fontes,
and
G.J.Davies
(2005).
How family 26 glycoside hydrolases orchestrate catalysis on different polysaccharides: structure and activity of a Clostridium thermocellum lichenase, CtLic26A.
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J Biol Chem,
280,
32761-32767.
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PDB codes:
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F.De Lemos Esteves,
T.Gouders,
J.Lamotte-Brasseur,
S.Rigali,
and
J.M.Frère
(2005).
Improving the alkalophilic performances of the Xyl1 xylanase from Streptomyces sp. S38: structural comparison and mutational analysis.
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Protein Sci,
14,
292-302.
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F.Löhr,
V.V.Rogov,
M.Shi,
F.Bernhard,
and
V.Dötsch
(2005).
Triple-resonance methods for complete resonance assignment of aromatic protons and directly bound heteronuclei in histidine and tryptophan residues.
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J Biomol NMR,
32,
309-328.
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H.Shibuya,
S.Kaneko,
and
K.Hayashi
(2005).
A single amino acid substitution enhances the catalytic activity of family 11 xylanase at alkaline pH.
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Biosci Biotechnol Biochem,
69,
1492-1497.
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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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M.T.Murakami,
R.Ruller,
R.J.Ward,
and
R.K.Arni
(2005).
Crystallization and preliminary X-ray crystallographic studies of the mesophilic xylanase A from Bacillus subtilis 1A1.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
219-220.
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F.Payan,
P.Leone,
S.Porciero,
C.Furniss,
T.Tahir,
G.Williamson,
A.Durand,
P.Manzanares,
H.J.Gilbert,
N.Juge,
and
A.Roussel
(2004).
The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases.
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J Biol Chem,
279,
36029-36037.
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PDB codes:
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F.Vincent,
T.M.Gloster,
J.Macdonald,
C.Morland,
R.V.Stick,
F.M.Dias,
J.A.Prates,
C.M.Fontes,
H.J.Gilbert,
and
G.J.Davies
(2004).
Common inhibition of both beta-glucosidases and beta-mannosidases by isofagomine lactam reflects different conformational itineraries for pyranoside hydrolysis.
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Chembiochem,
5,
1596-1599.
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PDB codes:
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F.de Lemos Esteves,
V.Ruelle,
J.Lamotte-Brasseur,
B.Quinting,
and
J.M.Frère
(2004).
Acidophilic adaptation of family 11 endo-beta-1,4-xylanases: modeling and mutational analysis.
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Protein Sci,
13,
1209-1218.
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G.Golan,
D.Shallom,
A.Teplitsky,
G.Zaide,
S.Shulami,
T.Baasov,
V.Stojanoff,
A.Thompson,
Y.Shoham,
and
G.Shoham
(2004).
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.
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J Biol Chem,
279,
3014-3024.
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PDB codes:
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H.Novoa De Armas,
C.Verboven,
C.De Ranter,
J.Desair,
A.Vande Broek,
J.Vanderleyden,
and
A.Rabijns
(2004).
Azospirillum irakense pectate lyase displays a toroidal fold.
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Acta Crystallogr D Biol Crystallogr,
60,
999.
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PDB code:
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N.Moiseeva,
and
M.Allaire
(2004).
Crystals of family 11 xylanase II from Trichoderma longibrachiatum that diffract to atomic resolution.
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Acta Crystallogr D Biol Crystallogr,
60,
1275-1277.
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A.J.Oakley,
T.Heinrich,
C.A.Thompson,
and
M.C.Wilce
(2003).
Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching.
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Acta Crystallogr D Biol Crystallogr,
59,
627-636.
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PDB code:
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A.Varrot,
and
G.J.Davies
(2003).
Direct experimental observation of the hydrogen-bonding network of a glycosidase along its reaction coordinate revealed by atomic resolution analyses of endoglucanase Cel5A.
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Acta Crystallogr D Biol Crystallogr,
59,
447-452.
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PDB codes:
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A.Varrot,
T.P.Frandsen,
H.Driguez,
and
G.J.Davies
(2002).
Structure of the Humicola insolens cellobiohydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-beta-cellobioside, at 1.9 A.
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Acta Crystallogr D Biol Crystallogr,
58,
2201-2204.
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PDB code:
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A.Vasella,
G.J.Davies,
and
M.Böhm
(2002).
Glycosidase mechanisms.
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Curr Opin Chem Biol,
6,
619-629.
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D.J.Vocadlo,
J.Wicki,
K.Rupitz,
and
S.G.Withers
(2002).
Mechanism of Thermoanaerobacterium saccharolyticum beta-xylosidase: kinetic studies.
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Biochemistry,
41,
9727-9735.
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D.Nurizzo,
T.Nagy,
H.J.Gilbert,
and
G.J.Davies
(2002).
The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A.
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Structure,
10,
547-556.
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PDB codes:
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S.J.Charnock,
I.E.Brown,
J.P.Turkenburg,
G.W.Black,
and
G.J.Davies
(2002).
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
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Proc Natl Acad Sci U S A,
99,
12067-12072.
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PDB codes:
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T.A.Tahir,
J.G.Berrin,
R.Flatman,
A.Roussel,
P.Roepstorff,
G.Williamson,
and
N.Juge
(2002).
Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger.
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J Biol Chem,
277,
44035-44043.
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E.Sabini,
K.S.Wilson,
S.Danielsen,
M.Schülein,
and
G.J.Davies
(2001).
Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
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Acta Crystallogr D Biol Crystallogr,
57,
1344-1347.
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PDB codes:
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J.M.van den Elsen,
D.A.Kuntz,
and
D.R.Rose
(2001).
Structure of Golgi alpha-mannosidase II: a target for inhibition of growth and metastasis of cancer cells.
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EMBO J,
20,
3008-3017.
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PDB codes:
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J.Wouters,
J.Georis,
D.Engher,
J.Vandenhaute,
J.Dusart,
J.M.Frere,
E.Depiereux,
and
P.Charlier
(2001).
Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38.
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Acta Crystallogr D Biol Crystallogr,
57,
1813-1819.
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PDB code:
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S.K.Das,
J.M.Mallet,
J.Esnault,
P.A.Driguez,
P.Duchaussoy,
P.Sizun,
J.P.Hérault,
J.M.Herbert,
M.Petitou,
and
P.Sinaÿ
(2001).
Synthesis of Conformationally Locked Carbohydrates: A Skew-Boat Conformation of L-Iduronic Acid Governs the Antithrombotic Activity of Heparin.
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Angew Chem Int Ed Engl,
40,
1670-1673.
|
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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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C.S.Rye,
and
S.G.Withers
(2000).
Glycosidase mechanisms.
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Curr Opin Chem Biol,
4,
573-580.
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U.M.Unligil,
and
J.M.Rini
(2000).
Glycosyltransferase structure and mechanism.
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Curr Opin Struct Biol,
10,
510-517.
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U.M.Unligil,
S.Zhou,
S.Yuwaraj,
M.Sarkar,
H.Schachter,
and
J.M.Rini
(2000).
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
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EMBO J,
19,
5269-5280.
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PDB codes:
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V.Notenboom,
S.J.Williams,
R.Hoos,
S.G.Withers,
and
D.R.Rose
(2000).
Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
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Biochemistry,
39,
11553-11563.
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PDB codes:
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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
