PDBsum entry: 1y4w

Hydrolase

PDB-id: 1y4w

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PROCHECK

Protein chain

517 a.a. *

Ligands

NAG-NAG

NAG ×3

GOL ×2

Waters ×921

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1y4w

Name:

Hydrolase

Title:

Crystal structure of exo-inulinase from aspergillus awamori in spacegroup p21

Structure:

Exo-inulinase. Chain: a. Ec: 3.2.1.80

Source:

Aspergillus awamori. Organism_taxid: 105351. Strain: 2250

UniProt:

Q96TU3 (Q96TU3_ASPAW)

Seq:

Struc:

Seq:

Struc:

Seq:

537 a.a.

Struc:

517 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.3.2.1.80   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Hydrolysis of terminal, non-reducing 2,1- and 2,6-linked beta-D-fructofuranose residues in fructans.

Pathway:

Fructosidase

Resolution:

1.55Å

R-factor:

0.171

R-free:

0.198

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:

01-Dec-04

Release date:

14-Dec-04

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Clefts

Surface

Key reference

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.