PDBsum entry 2c0h

Hydrolase

PDB id: 2c0h

Contents

Protein chain

353 a.a. *

Ligands

SO4

Waters ×203

* Residue conservation analysis

PDB id:

2c0h

Name:

Hydrolase

Title:

X-ray structure of beta-mannanase from blue mussel mytilus edulis

Structure:

Mannan endo-1,4-beta-mannosidase. Chain: a. Synonym: endo-beta-1,4-d-mannanases, beta-mannanase, mana. Engineered: yes. Mutation: yes

Source:

Mytilus edulis. Blue mussel. Organism_taxid: 6550. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

1.60Å R-factor: 0.191 R-free: 0.210

Authors:

A.M.Larsson,L.Anderson,B.Xu,I.G.Munoz,I.Uson,J.-C.Janson,H.Stalbrand, J.Stahlberg

Key ref:

A.M.Larsson et al. (2006). Three-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis. J Mol Biol, 357, 1500-1510. PubMed id: 16487541 DOI: 10.1016/j.jmb.2006.01.044

Date:

02-Sep-05 Release date: 22-Feb-06

Protein chain

Q8WPJ2  (MANA_MYTED) -  Mannan endo-1,4-beta-mannosidase from Mytilus edulis

Seq: 367 a.a.

Struc: 353 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.78 - mannan endo-1,4-beta-mannosidase.
• Reaction: Random hydrolysis of 1,4-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.

DOI no: 10.1016/j.jmb.2006.01.044

J Mol Biol 357:1500-1510 (2006)

PubMed id: 16487541

Three-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis.

A.M.Larsson, L.Anderson, B.Xu, I.G.Muñoz, I.Usón, J.C.Janson, H.Stålbrand, J.Ståhlberg.

ABSTRACT

Endo-beta-1,4-d-mannanase is the key depolymerizing enzyme for beta-1,4-mannan polymers present in the cell walls of plants and some algae, as well as in some types of plant seeds. Endo-1,4-beta-mannanase from blue mussel Mytilus edulis (MeMan5A) belongs to the glycoside hydrolase (GH) family 5 enzymes. The MeMan5A structure has been determined to 1.6A resolution using the multiple-wavelength anomalous dispersion method at the selenium K edge with selenomethionyl MeMan5A expressed in the yeast Pichia pastoris. As expected for GH 5 enzymes, the structure showed a (betaalpha)(8)-barrel fold. An unusually large number of histidine side-chains are exposed on the surface, which may relate to its location within the crystalline style of the digestive tract of the mussel. Kinetic analysis of MeMan5A revealed that the enzyme requires at least six subsites for efficient hydrolysis. Mannotetraose (M4) and mannopentaose (M5) were shown to interact with subsites -3 to +1, and -3 to +2, respectively. A clear kinetic threshold was observed when going from M4 to M5, indicating that the +2 subsite provides important interaction in the hydrolysis of short oligomeric mannose substrates. The catalytic centre motif at subsite -1 found in superfamily GH clan A is, as expected, conserved in MeMan5A, but the architecture of the catalytic cleft differs significantly from other GH 5 enzyme structures. We therefore suggest that MeMan5A represents a new subfamily in GH 5.

Selected figure(s)

Figure 3.
Figure 3. The M. edulis Man5A structure superimposed with (a) Thermobifida fusca Man5 in complex with mannotriose in subsites -2, -3 and -4, and with (b) and (c) Hypocrea jecorina Man5A in complex with mannobiose in subsites +1 and +2. M. edulis Man5A side-chains are coloured magenta, the other two enzymes are coloured dark blue and light blue, and the ligands are coloured gold. Except for the catalytic acid/base E117, none of the residues participating in the binding of the ligand in (a) and (c) is conserved in MeMan5A. In (b) the highly conserved residues at subsite -1, typical of clan GH A, are shown, numbered as in MeMan5A.

Figure 6.
Figure 6. The van der Waals surface of the MeMan5A structure with nitrogen atoms of histidine residues in blue and the oxygen atoms of the two catalytic residues in red.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 1500-1510) copyright 2006.

Figures were selected by the author.