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* Residue conservation analysis
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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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Gene Ontology (GO) functional annotation
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Biological process
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carbohydrate metabolic process
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1 term
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Biochemical function
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catalytic activity
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3 terms
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DOI no:
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Acta Crystallogr D Biol Crystallogr
59:1447-1453
(2003)
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PubMed id:
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Structure of xylanase Xys1delta from Streptomyces halstedii.
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A.Canals,
M.C.Vega,
F.X.Gomis-Rüth,
M.Díaz,
R.I.Santamaría R,
M.Coll.
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ABSTRACT
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Xylanases hydrolyze the beta-1,4-linked xylose backbone of xylans. They are of
increasing interest in the paper and food industries for their pre-bleaching and
bio-pulping applications. Such industries demand new xylanases to cover a wider
range of cleavage specificity, activity and stability. The catalytic domain of
xylanase Xys1 from Streptomyces halstedii JM8 was expressed, purified and
crystallized and native data were collected to 1.78 A resolution with an
R(merge) of 4.4%. The crystals belong to space group P2(1)2(1)2(1), with
unit-cell parameters a = 34.05, b = 79.60, c = 87.80 A. The structure was solved
by the molecular-replacement method using the structure of the homologue Xyl10A
from Streptomyces lividans. In a similar manner to other members of its family,
Xys1 folds to form a standard (beta/alpha)(8) barrel with the two catalytic
functions, the acid/base and the nucleophile, at its C-terminal side. The
overall structure is described and compared with those of related xylanases.
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Selected figure(s)
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Figure 2.
Figure 2 Ribbon representation of Xys1  .
For clarity, only the major secondary-structure elements forming
the (  /
 )[8]
barrel have been labelled. Additional minor helices are coloured
orange. (a) Side view of the catalytic domain, with the carbonyl
side of the -barrel
facing upwards. (b) Top view of the molecule.
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Figure 4.
Figure 4 Stereoviews of four structural details in the Xys1 structure.
(a) Active site of the enzyme, with the two catalytic glutamic
acid residues coloured red. (b) Conserved cis-peptide bond
between His80 and Thr81. (c) Double conformation at the
Cys168-Cys200 disulfide bond. (d) Magnesium-coordinating Leu302
at the C-terminal end of the polypeptide chain. The 2F[o] - F[c]
electron-density maps are contoured at the 1.0  level.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2003,
59,
1447-1453)
copyright 2003.
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Figures were
selected
by the author.
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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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G.Michel,
T.Tonon,
D.Scornet,
J.M.Cock,
and
B.Kloareg
(2010).
The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes.
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New Phytol, 188,
82-97.
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S.Najmudin,
B.A.Pinheiro,
M.J.Romão,
J.A.Prates,
and
C.M.Fontes
(2008).
Purification, crystallization and crystallographic analysis of Clostridium thermocellum endo-1,4-beta-D-xylanase 10B in complex with xylohexaose.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 64,
715-718.
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K.Manikandan,
A.Bhardwaj,
N.Gupta,
N.K.Lokanath,
A.Ghosh,
V.S.Reddy,
and
S.Ramakumar
(2006).
Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.
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Protein Sci, 15,
1951-1960.
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PDB codes:
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Ihsanawati,
T.Kumasaka,
T.Kaneko,
C.Morokuma,
R.Yatsunami,
T.Sato,
S.Nakamura,
and
N.Tanaka
(2005).
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
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Proteins, 61,
999.
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PDB codes:
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K.Manikandan,
A.Bhardwaj,
A.Ghosh,
V.S.Reddy,
and
S.Ramakumar
(2005).
Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 61,
747-749.
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T.Collins,
C.Gerday,
and
G.Feller
(2005).
Xylanases, xylanase families and extremophilic xylanases.
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FEMS Microbiol Rev, 29,
3.
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M.Díaz,
S.Rodriguez,
J.M.Fernández-Abalos,
J.De Las Rivas,
A.Ruiz-Arribas,
V.L.Shnyrov,
and
R.I.Santamaría
(2004).
Single mutations of residues outside the active center of the xylanase Xys1 Delta from Streptomyces halstedii JM8 affect its activity.
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FEMS Microbiol Lett, 240,
237-243.
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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
