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Carbohydrate-binding module
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PDB id
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1gny
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PDB id:
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Carbohydrate-binding module
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Title:
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Xylan-binding module cbm15
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Structure:
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Xylanase 10c. Chain: a. Fragment: carbohydrate binding module 15, residues (91-244). Engineered: yes
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Source:
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Pseudomonas cellulosa. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3-plyss.
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Resolution:
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1.63Å
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R-factor:
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0.152
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R-free:
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0.177
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Authors:
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S.Szabo,S.Jamal,H.Xie,S.J.Charnock,D.N.Bolam,H.J.Gilbert, G.J.Davies
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Key ref:
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L.Szabo
et al.
(2001).
Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation.
J Biol Chem,
276,
49061-49065.
PubMed id:
DOI:
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Date:
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10-Oct-01
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Release date:
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29-Nov-01
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PROCHECK
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Headers
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References
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Q59675
(Q59675_9GAMM) -
Endo-beta-1,4-xylanase (Precursor)
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Seq: Struc:
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606 a.a.
153 a.a.*
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Key: |
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PfamA domain |
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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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DOI no:
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J Biol Chem
276:49061-49065
(2001)
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PubMed id:
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Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation.
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L.Szabo,
S.Jamal,
H.Xie,
S.J.Charnock,
D.N.Bolam,
H.J.Gilbert,
G.J.Davies.
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ABSTRACT
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The recycling of photosynthetically fixed carbon by the action of microbial
glycoside hydrolases is a key biological process. The consortium of degradative
enzymes involved in this process frequently display catalytic modules appended
to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs play a
central role in the optimization of the catalytic activity of plant cell wall
hydrolases through their binding to specific plant structural polysaccharides.
Despite their pivotal role in the biodegradation of plant biomass, the mechanism
by which these proteins recognize their target ligands is unclear. This report
describes the structure of a xylan-binding CBM (CBM15) in complex with its
ligand. This module, derived from Pseudomonas cellulosa xylanase Xyn10C, binds
to both soluble xylan and xylooligosaccharides. The three-dimensional crystal
structure of CBM15 bound to xylopentaose has been solved by x-ray
crystallography to a resolution of 1.6 A. The protein displays a similar
beta-jelly roll fold to that observed in many other families of binding-modules.
A groove, 20-25 A in length, on the concave surface of one of the beta-sheets
presents two tryptophan residues, the faces of which are orientated at
approximately 240 degrees to one another. These form-stacking interactions with
the n and n+2 sugars of xylopentaose complementing the approximate 3-fold
helical structure of this ligand in the binding cleft of CBM15. In four of the
five observed binding subsites, the 2' and 3' hydroxyls of the bound ligand are
solvent-exposed, providing an explanation for the capacity of this xylan-binding
CBM to accommodate the highly decorated xylans found in the plant cell wall.
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Selected figure(s)
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Figure 1.
Fig. 1. The three-dimensional structure of the P.
cellulosa CBM15 in complex with xylopentaose. A displays the
overall secondary structure of the protein with the location of
bound xylopentaose. B shows the electron density of xylopentaose
bound to CBM15. The map shown is a maximum-likelihood/ [A]
weighted 2F[obs] F[calc]
synthesis (28) calculated at a contour level of ~0.6
electrons/Å2. This figure was made with
MOLSCRIPT/BOBSCRIPT (38, 39).
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Figure 2.
Fig. 2. Schematic diagram of the interactions of CBM15
with xylopentaose.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2001,
276,
49061-49065)
copyright 2001.
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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.Hervé,
A.Rogowski,
A.W.Blake,
S.E.Marcus,
H.J.Gilbert,
and
J.P.Knox
(2010).
Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects.
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Proc Natl Acad Sci U S A, 107,
15293-15298.
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F.Vincent,
A.Round,
A.Reynaud,
C.Bordi,
A.Filloux,
and
Y.Bourne
(2010).
Distinct oligomeric forms of the Pseudomonas aeruginosa RetS sensor domain modulate accessibility to the ligand binding site.
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Environ Microbiol, 12,
1775-1786.
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PDB code:
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G.Caprioli,
G.Cristalli,
E.Ragazzi,
L.Molin,
M.Ricciutelli,
G.Sagratini,
R.Seraglia,
Y.Zuo,
and
S.Vittori
(2010).
A preliminary matrix-assisted laser desorption/ionization time-of-flight approach for the characterization of Italian lentil varieties.
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Rapid Commun Mass Spectrom, 24,
2843-2848.
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C.Christiansen,
M.Abou Hachem,
S.Janecek,
A.Viksø-Nielsen,
A.Blennow,
and
B.Svensson
(2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
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FEBS J, 276,
5006-5029.
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C.Hervé,
A.Rogowski,
H.J.Gilbert,
and
J.Paul Knox
(2009).
Enzymatic treatments reveal differential capacities for xylan recognition and degradation in primary and secondary plant cell walls.
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Plant J, 58,
413-422.
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D.Dodd,
and
I.O.Cann
(2009).
Enzymatic deconstruction of xylan for biofuel production.
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Glob Change Biol Bioenergy, 1,
2.
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B.Granvogl,
V.Reisinger,
and
L.A.Eichacker
(2006).
Mapping the proteome of thylakoid membranes by de novo sequencing of intermembrane peptide domains.
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Proteomics, 6,
3681-3695.
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L.McCartney,
A.W.Blake,
J.Flint,
D.N.Bolam,
A.B.Boraston,
H.J.Gilbert,
and
J.P.Knox
(2006).
Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules.
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Proc Natl Acad Sci U S A, 103,
4765-4770.
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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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D.Shallom,
and
Y.Shoham
(2003).
Microbial hemicellulases.
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Curr Opin Microbiol, 6,
219-228.
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S.J.Charnock,
D.N.Bolam,
D.Nurizzo,
L.Szabó,
V.A.McKie,
H.J.Gilbert,
and
G.J.Davies
(2002).
Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose.
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Proc Natl Acad Sci U S A, 99,
14077-14082.
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PDB codes:
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I.Szabò,
F.Rigoni,
M.Bianchetti,
D.Carbonera,
F.Pierantoni,
R.Seraglia,
A.Segalla,
and
G.M.Giacometti
(2001).
Isolation and characterization of photosystem II subcomplexes from cyanobacteria lacking photosystem I.
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Eur J Biochem, 268,
5129-5134.
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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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