PDBsum entry: 1xyf

Hydrolase

PDB id: 1xyf

Contents

Protein chains

427 a.a. *

Waters ×493

* Residue conservation analysis

PDB id:

1xyf

Name:

Hydrolase

Title:

Endo-1,4-beta-xylanase from streptomyces olivaceoviridis

Structure:

Endo-1,4-beta-xylanase. Chain: a, b. Fragment: catalytic domain, xylan-binding domain. Ec: 3.2.1.8

Source:

Streptomyces olivaceoviridis. Organism_taxid: 1921. Strain: e-86

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.197 R-free: 0.235

Authors:

Z.Fujimoto,H.Mizuno,A.Kuno,I.Kusakabe

Key ref:

S.Kaneko et al. (1999). An investigation of the nature and function of module 10 in a family F/10 xylanase FXYN of Streptomyces olivaceoviridis E-86 by module shuffling with the Cex of Cellulomonas fimi and by site-directed mutagenesis. FEBS Lett, 460, 61-66. PubMed id: 10571062 DOI: 10.1016/S0014-5793(99)01318-6

Date:

11-May-99 Release date: 10-May-00

Protein chains

Q7SI98  (Q7SI98_STROI) -  Hydrolase

Seq: 436 a.a.

Struc: 427 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (5 terms)

DOI no: 10.1016/S0014-5793(99)01318-6

FEBS Lett 460:61-66 (1999)

PubMed id: 10571062

An investigation of the nature and function of module 10 in a family F/10 xylanase FXYN of Streptomyces olivaceoviridis E-86 by module shuffling with the Cex of Cellulomonas fimi and by site-directed mutagenesis.

S.Kaneko, A.Kuno, Z.Fujimoto, D.Shimizu, S.Machida, Y.Sato, K.Yura, M.Go, H.Mizuno, K.Taira, I.Kusakabe, K.Hayashi.

ABSTRACT

Although the amino acid homology in the catalytic domain of FXYN xylanase from Streptomyces olivaceoviridis E-86 and Cex xylanase from Cellulomonas fimi is only 50%, an active chimeric enzyme was obtained by replacing module 10 in FXYN with module 10 from Cex. In the family F/10 xylanases, module 10 is an important region as it includes an acid/base catalyst and a substrate binding residue. In FXYN, module 10 consists of 15 amino acid residues, while in Cex it consists of 14 amino acid residues. The Km and kcat values of the chimeric xylanase FCF-C10 for PNP-xylobioside (PNP-X2) were 10-fold less than those for FXYN. CD spectral data indicated that the structure of the chimeric enzyme was similar to that of FXYN. Based on the comparison of the amino acid sequences of FXYN and Cex in module 10, we constructed four mutants of FXYN. When D133 or S135 of FXYN was deleted, the kinetic properties were not changed from those of FXYN. By deletion of both D133 and S135, the Km value for PNP-X2 decreased from the 2.0 mM of FXYN to 0.6 mM and the kcat value decreased from the 20 s(-1) of FXYN to 8.7 s(-1). Insertion of Q140 into the doubly deleted mutant further reduced the Km value to 0.3 mM and the kcat value to 3.8 s(-1). These values are close to those for the chimeric enzyme FCF-C10. These results indicate that module 10 itself is able to accommodate changes in the sequence position of amino acids which are critical for enzyme function. Since changes of the spatial position of these amino acids would be expected to result in enzyme inactivation, module 10 must have some flexibility in its tertiary structure. The structure of module 10 itself also affects the substrate specificity of the enzyme.

Selected figure(s)

Figure 2.
Fig. 2. The substrate binding cleft of FXYN. The structure of FXYN was modeled by using the crystal structure of the xylanase A from Streptomyces lividans [28].

Figure 7.
Fig. 7. The environment of module 10 in FXYN and Cex. A: FXYN. B: Cex. Hydrogen bonds are shown as dashed lines. The numbers written beside hydrogen bonds indicate the distance between the atoms in Å. The structure of FXYN was modeled using the crystal structure of the xylanase A from Streptomyces lividans [28].

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (1999, 460, 61-66) copyright 1999.

Figures were selected by an automated process.