PDBsum entry: 1of3

Hydrolase/carbohydrate binding

PDB-id

1of3


	Main view

Contents

Description

Header details

Protein chains

Metal ions

_CA ×2

Waters ×283

* Residue conservation analysis

Tools

Image Generation

AstexViewer™@PDBe

Run PROCHECK

Clefts Calculation


Bottom view		Right view

PDB id:

1of3

Name:

Hydrolase/carbohydrate binding

Title:

Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, tmcbm27

Structure:

Beta-mannosidase. Chain: a, b. Fragment: carbohydrate-binding module, residues 505-680. Synonym: tmcbm27. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Expressed in: escherichia coli. Expression_system_taxid: 511693.

UniProt:

Chains A, B: Q9RIK9 (Q9RIK9_THEMA)

Seq:

Struc:

Seq:

Struc:

Seq:

680 a.a.

Struc:

176 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Resolution:

2.0Å

R-factor:

0.190

R-free:

0.225

Authors:

A.B.Boraston,T.J.Revett,C.M.Boraston,D.Nurizzo,G.J.Davies

Key ref:

A.B.Boraston et al. (2003). Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27.. Structure, 11, 665-675. [PubMed id: 12791255] [DOI: 10.1016/S0969-2126(03)00100-X]

Date:

07-Apr-03

Release date:

17-Apr-03

Related entries:

1of4 structural and thermodynamic dissection of specific mannan recognition by a carbohydrate -binding module, tmcbm27

Quick_links

RCSB

PDBe

SRS

MMDB

JenaLib

OCA

Proteopedia

CATH

SCOP

FSSP

HSSP

PDBSWS

PQS

ProSAT

Whatcheck

EDS

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/S0969-2126(03)00100-X Structure 11:665-675 (2003)

PubMed id: 12791255

Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27.

A.B.Boraston, T.J.Revett, C.M.Boraston, D.Nurizzo, G.J.Davies.

ABSTRACT

The C-terminal 176 amino acids of a Thermotoga maritima mannanase (Man5) constitute a carbohydrate binding module (CBM) that has been classified into CBM family 27. The isolated CBM27 domain, named TmCBM27, binds tightly (K(a)s 10(5)-10(6) M(-1)) to beta-1, 4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. The X-ray crystal structures of native TmCBM27, a TmCBM27-mannohexaose complex, and a TmCBM27-6(3),6(4)-alpha-D-galactosyl-mannopentaose complex at 2.0 A, 1.6 A, and 1.35 A, respectively, reveal the basis of TmCBM27's specificity for mannans. In particular, the latter complex, which is the first structure of a CBM in complex with a branched plant cell wall polysaccharide, illustrates how the architecture of the binding site can influence the recognition of naturally substituted polysaccharides.

Selected figure(s)

Figure 7.
Figure 7. A Schematic Showing the Interactions of TmCBM27 with G[2]M[5] (A) and Mannohexaose (B)Hydrogen bonds, dashed lines; water molecules, filled circles. Binding subsites referred to in the text are shown underneath the schematics with brackets.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 665-675) copyright 2003.

Figure was selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id Reference

19129644 M.Tanaka, Y.Umemoto, H.Okamura, D.Nakano, Y.Tamaru, and T.Araki (2009).
Cloning and characterization of a beta-1,4-mannanase 5C possessing a family 27 carbohydrate-binding module from a marine bacterium, Vibrio sp. strain MA-138.

Biosci Biotechnol Biochem, 73, 109-116.

19609934 N.Forsgren, R.J.Lamont, and K.Persson (2009).
Crystal structure of the variable domain of the Streptococcus gordonii surface protein SspB.

Protein Sci, 18, 1896-1905.

PDB code: 2wd6

16601125 J.Henshaw, A.Horne-Bitschy, A.L.van Bueren, V.A.Money, D.N.Bolam, M.Czjzek, N.A.Ekborg, R.M.Weiner, S.W.Hutcheson, G.J.Davies, A.B.Boraston, and H.J.Gilbert (2006).
Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.

J Biol Chem, 281, 17099-17107.

PDB codes: 2cdo 2cdp

16314409 S.Najmudin, C.I.Guerreiro, A.L.Carvalho, J.A.Prates, M.A.Correia, V.D.Alves, L.M.Ferreira, M.J.Romão, H.J.Gilbert, D.N.Bolam, and C.M.Fontes (2006).
Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains.

J Biol Chem, 281, 8815-8828.

PDB codes: 2c24 2c26 2c4x

15784618 J.Flint, D.N.Bolam, D.Nurizzo, E.J.Taylor, M.P.Williamson, C.Walters, G.J.Davies, and H.J.Gilbert (2005).
Probing the mechanism of ligand recognition in family 29 carbohydrate-binding modules.

J Biol Chem, 280, 23718-23726.

PDB codes: 1w8t 1w8u 1w8w 1w8z 1w90 1w9f 1wcu

16301796 P.Skubák, S.Ness, and N.S.Pannu (2005).
Extending the resolution and phase-quality limits in automated model building with iterative refinement.

Acta Crystallogr D Biol Crystallogr, 61, 1626-1635.

16237010 S.B.Conners, C.I.Montero, D.A.Comfort, K.R.Shockley, M.R.Johnson, S.R.Chhabra, and R.M.Kelly (2005).
An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima.

J Bacteriol, 187, 7267-7282.

15999223 Y.Hatada, N.Takeda, K.Hirasawa, Y.Ohta, R.Usami, Y.Yoshida, W.D.Grant, S.Ito, and K.Horikoshi (2005).
Sequence of the gene for a high-alkaline mannanase from an alkaliphilic Bacillus sp. strain JAMB-750, its expression in Bacillus subtilis and characterization of the recombinant enzyme.

Extremophiles, 9, 497-500.

15192099 A.L.Carvalho, A.Goyal, J.A.Prates, D.N.Bolam, H.J.Gilbert, V.M.Pires, L.M.Ferreira, A.Planas, M.J.Romão, and C.M.Fontes (2004).
The family 11 carbohydrate-binding module of Clostridium thermocellum Lic26A-Cel5E accommodates beta-1,4- and beta-1,3-1,4-mixed linked glucans at a single binding site.

J Biol Chem, 279, 34785-34793.

PDB code: 1v0a

15004012 D.N.Bolam, H.Xie, G.Pell, D.Hogg, G.Galbraith, B.Henrissat, and H.J.Gilbert (2004).
X4 modules represent a new family of carbohydrate-binding modules that display novel properties.

J Biol Chem, 279, 22953-22963.

15014076 F.M.Dias, F.Vincent, G.Pell, J.A.Prates, M.S.Centeno, L.E.Tailford, L.M.Ferreira, C.M.Fontes, G.J.Davies, and H.J.Gilbert (2004).
Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A.

J Biol Chem, 279, 25517-25526.

PDB code: 1uuq

15004011 J.L.Henshaw, D.N.Bolam, V.M.Pires, M.Czjzek, B.Henrissat, L.M.Ferreira, C.M.Fontes, and H.J.Gilbert (2004).
The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities.

J Biol Chem, 279, 21552-21559.

14670957 Z.Fujimoto, S.Kaneko, A.Kuno, H.Kobayashi, I.Kusakabe, and H.Mizuno (2004).
Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86.

J Biol Chem, 279, 9606-9614.

PDB codes: 1v6u 1v6v 1v6w 1v6x

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.