PDBsum entry: 1edt

Hydrolase (glucosidase)

PDB id: 1edt

Contents

Protein chain

265 a.a. *

Waters ×163

* Residue conservation analysis

PDB id:

1edt

Name:

Hydrolase (glucosidase)

Title:

Crystal structure of endo-beta-n-acetylglucosaminidase h at 1.9 angstroms resolution: active site geometry and substrate recognition

Structure:

Endo-beta-n-acetylglucosaminidase h, endo h. Chain: a. Engineered: yes

Source:

Streptomyces plicatus. Organism_taxid: 1922

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.199

Authors:

P.Van Roey,V.Rao

Key ref:

V.Rao et al. (1995). Crystal structure of endo-beta-N-acetylglucosaminidase H at 1.9 A resolution: active-site geometry and substrate recognition. Structure, 3, 449-457. PubMed id: 7663942 DOI: 10.1016/S0969-2126(01)00178-2

Date:

31-Mar-95 Release date: 04-Aug-95

Protein chain

P04067  (EBAG_STRPL) -  Endo-beta-N-acetylglucosaminidase H

Seq: 313 a.a.

Struc: 265 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.96 - Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase.
• Reaction: Endohydrolysis of the di-N-acetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn- structure. One N-acetyl-D-glucosamine residue remains attached to the protein; the rest of the oligosaccharide is released intact.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (6 terms)

DOI no: 10.1016/S0969-2126(01)00178-2

Structure 3:449-457 (1995)

PubMed id: 7663942

Crystal structure of endo-beta-N-acetylglucosaminidase H at 1.9 A resolution: active-site geometry and substrate recognition.

V.Rao, C.Guan, P.Van Roey.

ABSTRACT

BACKGROUND: Endo-beta-N-acetylglucosaminidase H (Endo H), an endoglycosidase secreted by Streptomyces plicatus, hydrolyzes the glycosidic bond between the core N-acetyglucosamine residues of asparagine-linked high-mannose oligosaccharides. Endo H is a commonly used reagent in glycobiology research, including the characterization of oligosaccharides in glycoproteins. On-going crystallographic studies of Endo H and related endoglycosidases are aimed at identifying the molecular features that determine the different substrate specificities of these enzymes. RESULTS: The three-dimensional structure of Endo H has been determined to 1.9 A resolution. The overall fold of the enzyme is that of an irregular (alpha/beta)8-barrel comprising eight beta-strand/loop/alpha-helix units. Units 5 and 6 have very short loop sections at the top of the molecule and their alpha-helices are replaced by sections of extended geometry. The loop of unit 2 includes a small two-stranded antiparallel beta-sheet. A shallow curved cleft runs across the surface of the molecule from the area of units 5 and 6, over the core of the beta-barrel to the area of the beta-sheet of loop 2. This cleft contains the putative catalytic residues Asp130 and Glu132 above the core of the beta-barrel. These residues are surrounded by several aromatic residues. The loop 2 area of the cleft is formed by neutral polar residues, mostly asparagines. CONCLUSIONS: The structure of Endo H is very similar to that of Endo F1, a closely related endoglycosidase secreted by Flavobacterium meningosepticum. Detailed comparison of the structures of Endo H and Endo F1 supports the model previously proposed for substate binding and recognition, in which the area of loop 2 determines the substrate specificity and the alpha-helices of units 5 and 6 are missing to accommodate the protein moiety of the substrate.

Selected figure(s)

Figure 4.
Figure 4. Schematic diagram showing the hydrogen-bonding pattern of the β-barrel. The residues that have their side chains pointing into the barrel are labeled. The broken lines represent hydrogen bonds. Nine strands are shown, the first one being duplicated. Pro213, indicated in bold, causes a kink in β-strand 7, disrupting the regular hydrogen-bonding pattern. Figure 4. Schematic diagram showing the hydrogen-bonding pattern of the β-barrel. The residues that have their side chains pointing into the barrel are labeled. The broken lines represent hydrogen bonds. Nine strands are shown, the first one being duplicated. Pro213, indicated in bold, causes a kink in β-strand 7, disrupting the regular hydrogen-bonding pattern.

Figure 5.
Figure 5. Stereo figure of the space-filling model of the top surface of Endo H in the same orientation as in Figure 3. The oligosaccharide-binding cleft runs from the bottom of the figure to the upper left corner. The catalytic residues, Asp130 and Glu132, are located close to the center in the lower left quadrant and are surrounded by many aromatic residues. Residues are color-coded in this and all subsequent figures as follows: Phe, Trp, Tyr in magenta; Asp, Glu in red; Ser, Thr, Asn, Gln in cyan; Arg, Lys, His in blue; Pro, Val, Ala, Ile, Leu in brown and Gly in white. Figure 5. Stereo figure of the space-filling model of the top surface of Endo H in the same orientation as in [3]Figure 3. The oligosaccharide-binding cleft runs from the bottom of the figure to the upper left corner. The catalytic residues, Asp130 and Glu132, are located close to the center in the lower left quadrant and are surrounded by many aromatic residues. Residues are color-coded in this and all subsequent figures as follows: Phe, Trp, Tyr in magenta; Asp, Glu in red; Ser, Thr, Asn, Gln in cyan; Arg, Lys, His in blue; Pro, Val, Ala, Ile, Leu in brown and Gly in white.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 449-457) copyright 1995.

Figures were selected by an automated process.