PDBsum entry: 1y9g

Hydrolase

PDB id: 1y9g

Contents

Protein chain

517 a.a. *

Ligands

NAG-NAG

NAG ×3

FRU

Waters ×755

* Residue conservation analysis

PDB id:

1y9g

Name:

Hydrolase

Title:

Crystal structure of exo-inulinase from aspergillus awamori with fructose

Structure:

Exo-inulinase. Chain: a. Fragment: sequence database residues 20-537. Ec: 3.2.1.80

Source:

Aspergillus awamori. Organism_taxid: 105351. Strain: 2250

Resolution:

1.87Å R-factor: 0.151 R-free: 0.195

Authors:

R.A.P.Nagem,A.L.Rojas,A.M.Golubev,O.S.Korneeva,E.V.Eneyskaya A.A.Kulminskaya,K.N.Neustroev,I.Polikarpov

Key ref:

R.A.Nagem et al. (2004). Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition. J Mol Biol, 344, 471-480. PubMed id: 15522299 DOI: 10.1016/j.jmb.2004.09.024

Date:

15-Dec-04 Release date: 21-Dec-04

Protein chain

Q96TU3  (Q96TU3_ASPAW) -  Exo-inulinase (Precursor)

Seq: 537 a.a.

Struc: 517 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.80 - Fructan beta-fructosidase.
• Pathway: Fructosidase
• Reaction: Hydrolysis of terminal, non-reducing 2,1- and 2,6-linked beta-D-fructofuranose residues in fructans.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: hydrolase activity (4 terms)

DOI no: 10.1016/j.jmb.2004.09.024

J Mol Biol 344:471-480 (2004)

PubMed id: 15522299

Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition.

R.A.Nagem, A.L.Rojas, A.M.Golubev, O.S.Korneeva, E.V.Eneyskaya, A.A.Kulminskaya, K.N.Neustroev, I.Polikarpov.

ABSTRACT

Exo-inulinases hydrolyze terminal, non-reducing 2,1-linked and 2,6-linked beta-d-fructofuranose residues in inulin, levan and sucrose releasing beta-d-fructose. We present the X-ray structure at 1.55A resolution of exo-inulinase from Aspergillus awamori, a member of glycoside hydrolase family 32, solved by single isomorphous replacement with the anomalous scattering method using the heavy-atom sites derived from a quick cryo-soaking technique. The tertiary structure of this enzyme folds into two domains: the N-terminal catalytic domain of an unusual five-bladed beta-propeller fold and the C-terminal domain folded into a beta-sandwich-like structure. Its structural architecture is very similar to that of another member of glycoside hydrolase family 32, invertase (beta-fructosidase) from Thermotoga maritima, determined recently by X-ray crystallography The exo-inulinase is a glycoprotein containing five N-linked oligosaccharides. Two crystal forms obtained under similar crystallization conditions differ by the degree of protein glycosylation. The X-ray structure of the enzyme:fructose complex, at a resolution of 1.87A, reveals two catalytically important residues: Asp41 and Glu241, a nucleophile and a catalytic acid/base, respectively. The distance between the side-chains of these residues is consistent with a double displacement mechanism of reaction. Asp189, which is part of the Arg-Asp-Pro motif, provides hydrogen bonds important for substrate recognition.

Selected figure(s)

Figure 4.
Figure 4. (a) Stereoview of fructose:enzyme interactions in the catalytic site of exo-inulinase. The fructose and the neighboring residues are shown. An omit electron density map (mF[obs] -DF[calc], calc), contoured at 3s, is displayed around the catalytic site of EI. (b) Schematic design of the interactions between the active-site residues and the fructose molecule (in pink). Hydrogen bonds are shown as cyan dotted lines. The Figure was drawn using the program LIGPLOT.56

Figure 5.
Figure 5. A representation of a double displacement mechanism of reaction with an overall retention of the configuration at the anomeric carbon atom of the substrate, catalysed by exo-inulinase from Aspergillus awamori. The R group may represent fructose units of inulin.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 344, 471-480) copyright 2004.

Figures were selected by an automated process.