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PDBsum entry 1of4
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Hydrolase/carbohydrate binding PDB id
1of4

 

 

 

 

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Contents
Protein chain
171 a.a. *
Ligands
BMA-BMA-BMA-BMA-
BMA
GOL ×2
Metals
_CA
Waters ×108
* Residue conservation analysis
PDB id:
1of4
Name: Hydrolase/carbohydrate binding
Title: Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, tmcbm27
Structure: Beta-mannosidase. Chain: a. 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.
Resolution:
1.60Å     R-factor:   0.165     R-free:   0.206
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q9RIK9  (Q9RIK9_THEMT) -  Beta-mannosidase from Thermotoga maritima
Seq:
Struc: 		 
Seq:
Struc: 		680 a.a.
171 a.a.
Key:    Secondary structure  CATH domain

 

 
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
21460451 N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and R.A.de Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.
  Acta Crystallogr D Biol Crystallogr, 67, 331-337.  
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
  Acta Crystallogr D Biol Crystallogr, 66, 783-788.  
20659281 S.E.Marcus, A.W.Blake, T.A.Benians, K.J.Lee, C.Poyser, L.Donaldson, O.Leroux, A.Rogowski, H.L.Petersen, A.Boraston, H.J.Gilbert, W.G.Willats, and J.P.Knox (2010).
Restricted access of proteins to mannan polysaccharides in intact plant cell walls.
  Plant J, 64, 191-203.  
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.

 

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