PDBsum entry 1gmm

Xylanase

PDB id: 1gmm

Contents

Protein chain

126 a.a. *

Ligands

SO4

Metals

_CA

_NA

Waters ×180

* Residue conservation analysis

PDB id:

1gmm

Name:

Xylanase

Title:

Carbohydrate binding module cbm6 from xylanase u clostridium thermocellum

Structure:

Cbm6. Chain: a. Fragment: xylan binding module (domain), residue 248-380. Engineered: yes

Source:

Clostridium thermocellum. Organism_taxid: 1515. Strain: f1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.208 R-free: 0.216

Authors:

M.Czjzek,A.Mosbah,D.Bolam,J.Allouch,V.Zamboni,B.Henrissat,H.J.Gilbert

Key ref:

M.Czjzek et al. (2001). The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved. J Biol Chem, 276, 48580-48587. PubMed id: 11673472 DOI: 10.1074/jbc.M109142200

Date:

19-Sep-01 Release date: 28-Nov-01

Protein chain

O52780  (O52780_ACETH) -  endo-1,4-beta-xylanase from Acetivibrio thermocellus

Seq: 683 a.a.

Struc: 126 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.8 - endo-1,4-beta-xylanase.
• Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

DOI no: 10.1074/jbc.M109142200

J Biol Chem 276:48580-48587 (2001)

PubMed id: 11673472

The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.

M.Czjzek, D.N.Bolam, A.Mosbah, J.Allouch, C.M.Fontes, L.M.Ferreira, O.Bornet, V.Zamboni, H.Darbon, N.L.Smith, G.W.Black, B.Henrissat, H.J.Gilbert.

ABSTRACT

Polysaccharide-degrading enzymes are generally modular proteins that contain non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity of the catalytic module. CBMs have been grouped into sequence-based families, and three-dimensional structural data are available for half of these families. Clostridium thermocellum xylanase 11A is a modular enzyme that contains a CBM from family 6 (CBM6), for which no structural data are available. We have determined the crystal structure of this module to a resolution of 2.1 A. The protein is a beta-sandwich that contains two potential ligand-binding clefts designated cleft A and B. The CBM interacts primarily with xylan, and NMR spectroscopy coupled with site-directed mutagenesis identified cleft A, containing Trp-92, Tyr-34, and Asn-120, as the ligand-binding site. The overall fold of CBM6 is similar to proteins in CBM families 4 and 22, although surprisingly the ligand-binding site in CBM4 and CBM22 is equivalent to cleft B in CBM6. These structural data define a superfamily of CBMs, comprising CBM4, CBM6, and CBM22, and demonstrate that, although CBMs have evolved from a relatively small number of ancestors, the structural elements involved in ligand recognition have been assembled at different locations on the ancestral scaffold.

Selected figure(s)

Figure 1.
Fig. 1. Electron density map at 2.1 Å and the final structural model represented as sticks. a, final electron density map, contoured at a 1 level, in the region of Tyr-34 and Trp-92, also showing the putative sodium ion. b, electron density map (1 level) showing the presence of a structural calcium ion bridging the N- and C-terminal ends. The figures were produced using the program TURBO-FRODO (26).

Figure 2.
Fig. 2. Ribbon and surface representations of CBM6. a, view showing the ligand-binding cleft (cleft A) formed by the loops between the two -sheets of the sandwich fold. b, surface representation of CBM6 in the same orientation as in a. The shallow binding cleft on top of the globular molecule is formed by Tyr-34 and Trp-92. c, ribbon representation of CBM6 in a perpendicular view with respect to a, showing the second possible cleft (cleft B), which is obstructed by a short loop in CBM6, situated on the concave face of the -sheet sandwich. a and c were produced with Molscript (45) and Raster3D (46), whereas b was produced using GRASP (47).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 48580-48587) copyright 2001.

Figures were selected by the author.