PDBsum entry 2d22

Hydrolase

PDB id: 2d22

Contents

Protein chains

427 a.a.

Ligands

XYS-XYS ×2

SO4 ×5

GOL ×8

Waters ×863

References listed in PDB file

Key reference

Title

Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from streptomyces olivaceoviridis e-86.

Authors

R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, A.Kuno.

Ref.

J Biochem (tokyo), 2009, 146, 61-70.

PubMed id

19279191

Abstract

Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.

Secondary reference #1

Title

Crystal structure of streptomyces olivaceoviridis e-86 beta-Xylanase containing xylan-Binding domain.

Authors

Z.Fujimoto, A.Kuno, S.Kaneko, S.Yoshida, H.Kobayashi, I.Kusakabe, H.Mizuno.

Ref.

J Mol Biol, 2000, 300, 575-585. [DOI no: 10.1006/jmbi.2000.3877]

PubMed id

10884353

Figure 6.
Figure 6. Stereoview of xylotriose docking model in subdomain b of XBD. The xylotriose structure was built based on the X-ray structure of b-1,4-xylan hydrate [Neduszynski and Marchessault 1972] and fitted into the binding site manually. Sugars are numbered from the non-reducing end. XBD residues interact with the 2nd xylose sugar through five hydrogen bonds (broken lines). The 2nd and 3rd sugar rings are placed over the aromatic rings of Tyr380 and Trp383.

Figure 7.
Figure 7. Stereoview of an interacting region between the catalytic domain (green) and XBD (subdomains a, blue; b, yellow; g, pink) superimposed on the equivalent region of the catalytic domain in Cex (white; 2exo; [White et al 1994]). Five inferred hydrogen bonding interactions between the triple Ser sequence in the N-terminal end of Ca7 and Asp354 in XBD are shown as blue broken lines. The difference between FXYN and Cex is clearly seen in the region from Cb7 to Ca7.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Crystal structures of the sugar complexes of streptomyces olivaceoviridis e-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module.

Authors

Z.Fujimoto, A.Kuno, S.Kaneko, H.Kobayashi, I.Kusakabe, H.Mizuno.

Ref.

J Mol Biol, 2002, 316, 65-78. [DOI no: 10.1006/jmbi.2001.5338]

PubMed id

11829503

Figure 1.
Figure 1. Stereo view of the ribbon model of FXYN/X2 complex. The catalytic domain, linker, and subdomains a, b, g of XBD are drawn in green, black, blue, yellow and pink, respectively. Two catalytic residues are displayed in red. Soaked xylose units and disulfide bonds are indicated by ball-and-stick drawings. The figure was drawn with the program Raster3d.[46 and 47]

Figure 5.
Figure 5. Stereo views of the sugar binding structures in the XBD with the F[obs] - F[calc] omit electron density maps contoured at 3s. (a) In the subdomain a in the FXYN/X2 complex, (b) subdomain g in the FXYN/X3 complex, (c) subdomain g in the FXYN/Glc complex, (d) subdomain a in the FXYN/Gal complex, (e) subdomain g in the FXYN/Lac complex, and (f) subdomain a in the FXYN/Lac complex from a different view point. Hydrogen bonding interactions between the enzyme and sugars are indicated by broken lines. Carbon numbers of bound xylose are indicated.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #3

Title

Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from streptomyces olivaceoviridis e-86.

Authors

Z.Fujimoto, S.Kaneko, A.Kuno, H.Kobayashi, I.Kusakabe, H.Mizuno.

Ref.

J Biol Chem, 2004, 279, 9606-9614. [DOI no: 10.1074/jbc.M312293200]

PubMed id

14670957

Figure 2.
FIG. 2. Stereo view of the bound decorated xylooligosaccharides in the catalytic cleft, with the F[obs] - F[calc] omit electron density maps contoured at 2.5 for the decorated xylooligosaccharides in the (-) side of the cleft. A, SoXyn10A·Araf-X3 complex. B, SoXyn10A·MeGlcUA-X3 complex. Hydrogen bonding interactions between the enzyme and sugars are indicated by broken lines.

Figure 6.
FIG. 6. Stereo views of Araf-X3. A, Araf-X3 bound in the catalytic cleft; B, Araf-X3 bound in subdomain of SoCBM13, with the F[obs] - F[calc] omit electron density maps contoured at 2.5 . The intramolecular hydrogen bond is shown as a broken line.

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #4

Title

Pcr cloning and expression of the f/10 family xylanse gene from streptomyces olivaceoviridis e-86

Authors

A.Kuno, D.Shimizu, S.Kaneko, Y.Koyama, S.Yoshida, H.Kobayashi, K.Hayashi, K.Taira, I.Kusakabe.

Ref.

J FERMENT BIOENG, 1998, 86, 434-439.

Secondary reference #5

Title

Significant enhancement in the binding of p-Nitrophenyl-Beta-D-Xylobioside by the e128h mutant f/10 xylanase from streptomyces olivaceoviridis e-86.

Authors

A.Kuno, D.Shimizu, S.Kaneko, T.Hasegawa, Y.Gama, K.Hayashi, I.Kusakabe, K.Taira.

Ref.

FEBS Lett, 1999, 450, 299-305. [DOI no: 10.1016/S0014-5793(99)00498-6]

PubMed id

10359093

Figure 4.
Fig. 4. Difference between hydrolysis rates of wt FXYN and E128H FXYN in the presence of either 2 mM of pNP-X[2] (a) or 3 μM of pNP-X[2] (b).

Figure 6.
Fig. 6. Schematic representation of the relative energies for reactions catalyzed by wt FXYN (broken line) and E128H FXYN (solid line).

The above figures are reproduced from the cited reference with permission from the Federation of European Biochemical Societies