PDBsum entry: 1v6u

Hydrolase

PDB-id: 1v6u

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

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Description

Header details

Header records

References

PROCHECK

Protein chains

436 a.a. *

Ligands

XYP-XYP ×4

XYP ×2

XYS

AHR-XYP-XYP ×2

Waters ×629

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1v6u

Name:

Hydrolase

Title:

Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with 2(2)-alpha-l- arabinofuranosyl-xylobiose

Structure:

Endo-1,4-beta-d-xylanase. Chain: a, b. Engineered: yes

Source:

Streptomyces olivaceoviridis. Organism_taxid: 1921. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: Q7SI98 (Q7SI98_STROI)

Seq:

Struc:

Seq:

436 a.a.

Struc:

436 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.10Å

R-factor:

0.212

R-free:

0.253

Authors:

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

Key ref:

Z.Fujimoto et al. (2004). Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86.. J Biol Chem, 279, 9606-9614. [PubMed id: 14670957] [DOI: 10.1074/jbc.M312293200]

Date:

04-Dec-03

Release date:

27-Apr-04

Related entries:

1xyf
the same protein, non-complexed structure
1isw
the same protein complexed with xylobiose
1v6v
the same protein complexed with 3(2)-alpha-l-
arabinofuranosyl-xylotriose
1v6w
the same protein complexed with 2(2)-4-o-methyl-alpha-d-
glucuronosyl-xylobiose
... plus others (see Header records)

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Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M312293200

J Biol Chem 279:9606-9614 (2004)

PubMed id: 14670957

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

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

ABSTRACT

The family 10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A) consists of a GH10 catalytic domain, which is joined by a Gly/Pro-rich linker to a family 13 carbohydrate-binding module (CBM13) that interacts with xylan. To understand how GH10 xylanases and CBM13 recognize decorated xylans, the crystal structure of SoXyn10A was determined in complex with alpha-l-arabinofuranosyl- and 4-O-methyl-alpha-d-glucuronosyl-xylooligosaccharides. The bound sugars were observed in the subsites of the catalytic cleft and also in subdomains alpha and gamma of CBM13. The data reveal that the binding mode of the oligosaccharides in the active site of the catalytic domain is entirely consistent with the substrate specificity and, in conjunction with the accompanying paper, demonstrate that the accommodation of the side chains in decorated xylans is conserved in GH10 xylanases of SoXyn10A against arabinoglucuronoxylan. CBM13 was shown to bind xylose or xylooligosaccharides reversibly by using nonsymmetric sugars as the ligands. The independent multiple sites in CBM13 may increase the probability of substrate binding.

Selected figure(s)

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 reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 9606-9614) copyright 2004.

Figures were selected by an automated process.