PDBsum entry: 1o7a

Hydrolase

PDB id: 1o7a

Contents

Protein chains

(+ 0 more) 484 a.a. *

Ligands

GDL ×6

NAG-NAG ×6

NAG ×6

EDO ×15

Waters ×2326

* Residue conservation analysis

PDB id:

1o7a

Name:

Hydrolase

Title:

Human beta-hexosaminidase b

Structure:

Beta-hexosaminidase beta chain. Chain: a, b, c, d, e, f. Fragment: 42-556. Synonym: beta-n-acetylhexosaminidase, hexosaminidase b, n-acetyl-beta-glucosaminidase. Engineered: yes. Other_details: recombinantly expressed fragment composed of residues 42-556, n-terminus of mature human enzyme is between residue 48 - 50

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf21.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.25Å R-factor: 0.196 R-free: 0.236

Authors:

T.Maier,N.Strater,C.Schuette,R.Klingenstein,K.Sandhoff, W.Saenger

Key ref:

T.Maier et al. (2003). The X-ray crystal structure of human beta-hexosaminidase B provides new insights into Sandhoff disease. J Mol Biol, 328, 669-681. PubMed id: 12706724 DOI: 10.1016/S0022-2836(03)00311-5

Date:

29-Oct-02 Release date: 23-Oct-03

Protein chains

P07686  (HEXB_HUMAN) -  Beta-hexosaminidase subunit beta

Seq: 556 a.a.

Struc: 484 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.52 - Beta-N-acetylhexosaminidase.
• Reaction: Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1016/S0022-2836(03)00311-5

J Mol Biol 328:669-681 (2003)

PubMed id: 12706724

The X-ray crystal structure of human beta-hexosaminidase B provides new insights into Sandhoff disease.

T.Maier, N.Strater, C.G.Schuette, R.Klingenstein, K.Sandhoff, W.Saenger.

ABSTRACT

Human lysosomal beta-hexosaminidases are dimeric enzymes composed of alpha and beta-chains, encoded by the genes HEXA and HEXB. They occur in three isoforms, the homodimeric hexosaminidases B (betabeta) and S (alphaalpha), and the heterodimeric hexosaminidase A (alphabeta), where dimerization is required for catalytic activity. Allelic variations in the HEXA and HEXB genes cause the fatal inborn errors of metabolism Tay-Sachs disease and Sandhoff disease, respectively. Here, we present the crystal structure of a complex of human beta-hexosaminidase B with a transition state analogue inhibitor at 2.3A resolution (pdb 1o7a). On the basis of this structure and previous studies on related enzymes, a retaining double-displacement mechanism for glycosyl hydrolysis by beta-hexosaminidase B is proposed. In the dimer structure, which is derived from an analysis of crystal packing, most of the mutations causing late-onset Sandhoff disease reside near the dimer interface and are proposed to interfere with correct dimer formation. The structure reported here is a valid template also for the dimeric structures of beta-hexosaminidase A and S.

Selected figure(s)

Figure 1.
Figure 1. Fold and homologues of human b-hexosaminidase B. (a) Schematic topogram, a-helices are represented by circles, b-strands by triangles, numbers indicate the position in protein sequence. Glycosylation sites (hexagons), disulfide bonds (red lines), proteolytic cleavage sites of the mature human enzyme ( ) and active-site residues (yellow circles) are indicated. (b) Ribbon diagram (stereo), N and C termini and proteolytic cleavage sites of processed HexB (107 -- 122, 311 -- 315) are indicated. In (a) and (b) the N-terminal domain is shown in orange (sheets) and red (helices), the C-terminal domain in green and cyan (strands and helices of central (b,a)8-barrel) and blue (extensions). In (b) the bound d-lactone inhibitor is shown in red. (c) Least-squares superposition of hHexB (blue) with SpHex (green; pdb 1hp5) shown in cartoon representation. The view is identical with that in (b). (d) Least-squares super- position (stereo) of the active-site residues of hHexB (blue) in complex with d-lactone, SpHex (green; pdb 1hp5) with the bound substrate chitobiose and SmChb (gold; pdb 1qbb) in complex with NAG-thiazoline. Residue labels relate to hHexB.

Figure 3.
Figure 3. Catalytic mechanism of human b-hexosaminidase B. The sketch in the upper panel illustrates the two-step double-displacement mechanism: in the first step (1a, 1b) (R = carbohydrate) a substrate- mediated nucleophilic attack on C1 is assisted by the general acid -- base catalyst Glu355 and releases the residual carbohydrate R via the formation of a cyclic oxa- zolinium intermediate. In the second step (2a, 2b) (R = H) a water molecule activated by Glu355 carries out a nucleophilic attack on C1 to open the oxazolinium ring, thereby retaining the initial configuration at C1. In the lower panel, all steps of the mechanism are illustrated by X-ray crystal structures: (a) SmChb together with the substrate chitobiose (pdb 1qbb); (b) hHexB in complex with d-lactone inhibitor (this work); (c) SpHex in complex with NAG-thiazoline; here, the water position is occupied by a glycerol molecule (pdb 1hp5).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 669-681) copyright 2003.

Figures were selected by an automated process.