PDBsum entry 1nae

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
Jmol PyMol
Protein chain
129 a.a. *
Waters ×181
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of cscbm6-3 from clostridium stercorarium in complex with xylotriose
Structure: Putative xylanase. Chain: a. Fragment: c-terminal carbohydrate-binding module. Engineered: yes
Source: Clostridium stercorarium. Organism_taxid: 1510. Gene: putative xylanase. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.05Å     R-factor:   0.137     R-free:   0.195
Authors: A.B.Boraston,V.Notenboom,R.A.J.Warren,D.G.Kilburn,D.R.Rose, G.Davies
Key ref:
A.B.Boraston et al. (2003). Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains. J Mol Biol, 327, 659-669. PubMed id: 12634060 DOI: 10.1016/S0022-2836(03)00152-9
27-Nov-02     Release date:   18-Mar-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8GJ44  (XYNA1_CLOSR) -  Endo-1,4-beta-xylanase A
651 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  


DOI no: 10.1016/S0022-2836(03)00152-9 J Mol Biol 327:659-669 (2003)
PubMed id: 12634060  
Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains.
A.B.Boraston, V.Notenboom, R.A.Warren, D.G.Kilburn, D.R.Rose, G.Davies.
Carbohydrate-binding polypeptides, including carbohydrate-binding modules (CBMs) from polysaccharidases, and lectins, are widespread in nature. Whilst CBMs are classically considered distinct from lectins, in that they are found appended to polysaccharide-degrading enzymes, this distinction is blurring. The crystal structure of CsCBM6-3, a "sequence-family 6" CBM in a xylanase from Clostridium stercorarium, at 2.3 A reveals a similar, all beta-sheet fold to that from MvX56, a module found in a family 33 glycoside hydrolase sialidase from Micromonospora viridifaciens, and the lectin AAA from Anguilla anguilla. Sequence analysis leads to the classification of MvX56 and AAA into a family distinct from that containing CsCBM6-3. Whilst these polypeptides are similar in structure they have quite different carbohydrate-binding specificities. AAA is known to bind fucose; CsCBM6-3 binds cellulose, xylan and other beta-glucans. Here we demonstrate that MvX56 binds galactose, lactose and sialic acid. Crystal structures of CsCBM6-3 in complex with xylotriose, cellobiose, and laminaribiose, 2.0 A, 1.35 A, and 1.0 A resolution, respectively, reveal that the binding site of CsCBM6-3 resides on the same polypeptide face as for MvX56 and AAA. Subtle differences in the ligand-binding surface give rise to the different specificities and biological activities, further blurring the distinction between classical lectins and CBMs.
  Selected figure(s)  
Figure 6.
Figure 6. Overlap of xylotriose (blue), cellobiose (green), and laminaribiose (yellow) bound to CsCBM6-3. Proline 138 is shown in ball-and-stick format. Bound calcium is shown as a large blue sphere.
Figure 7.
Figure 7. Overlap of the structure of CsCBM6-3 in complex with xylotriose (blue), MvX56 from the M. viridifaciens sialidase in complex with galactose (green), and A. anguilla agglutinin in complex with fucose (khaki). Metal ions are shown as spheres. The superimposition was prepared with SWISS-Pdb viewer.[23.]
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 659-669) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19422833 E.Ficko-Blean, and A.B.Boraston (2009).
N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.
  J Mol Biol, 390, 208-220.
PDB codes: 2w1q 2w1s 2w1u 2wdb
19240276 G.Michel, T.Barbeyron, B.Kloareg, and M.Czjzek (2009).
The family 6 carbohydrate-binding modules have coevolved with their appended catalytic modules toward similar substrate specificity.
  Glycobiology, 19, 615-623.  
18004751 J.W.Torrance, M.W.Macarthur, and J.M.Thornton (2008).
Evolution of binding sites for zinc and calcium ions playing structural roles.
  Proteins, 71, 813-830.  
16987809 A.B.Boraston, D.Wang, and R.D.Burke (2006).
Blood group antigen recognition by a Streptococcus pneumoniae virulence factor.
  J Biol Chem, 281, 35263-35271.
PDB codes: 2j1r 2j1s 2j1t 2j1u 2j1v 2j22
16990278 E.Ficko-Blean, and A.B.Boraston (2006).
The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor.
  J Biol Chem, 281, 37748-37757.
PDB codes: 2j1a 2j1e 2j7m
16251191 E.W.Odom, and G.R.Vasta (2006).
Characterization of a binary tandem domain F-type lectin from striped bass (Morone saxatilis).
  J Biol Chem, 281, 1698-1713.  
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
16707677 L.E.Taylor, B.Henrissat, P.M.Coutinho, N.A.Ekborg, S.W.Hutcheson, and R.M.Weiner (2006).
Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T.
  J Bacteriol, 188, 3849-3861.  
16436117 M.E.Nielsen, and M.D.Esteve-Gassent (2006).
The eel immune system: present knowledge and the need for research.
  J Fish Dis, 29, 65-78.  
17005007 M.S.Centeno, A.Goyal, J.A.Prates, L.M.Ferreira, H.J.Gilbert, and C.M.Fontes (2006).
Novel modular enzymes encoded by a cellulase gene cluster in Cellvibrio mixtus.
  FEMS Microbiol Lett, 265, 26-34.  
15501830 A.L.van Bueren, C.Morland, H.J.Gilbert, and A.B.Boraston (2005).
Family 6 carbohydrate binding modules recognize the non-reducing end of beta-1,3-linked glucans by presenting a unique ligand binding surface.
  J Biol Chem, 280, 530-537.
PDB codes: 1w9s 1w9t 1w9w
15866877 H.Ichinose, M.Yoshida, T.Kotake, A.Kuno, K.Igarashi, Y.Tsumuraya, M.Samejima, J.Hirabayashi, H.Kobayashi, and S.Kaneko (2005).
An exo-beta-1,3-galactanase having a novel beta-1,3-galactan-binding module from Phanerochaete chrysosporium.
  J Biol Chem, 280, 25820-25829.  
16239725 S.L.Newstead, J.N.Watson, A.J.Bennet, and G.Taylor (2005).
Galactose recognition by the carbohydrate-binding module of a bacterial sialidase.
  Acta Crystallogr D Biol Crystallogr, 61, 1483-1491.
PDB code: 2bzd
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.  
15242594 S.Jamal-Talabani, A.B.Boraston, J.P.Turkenburg, N.Tarbouriech, V.M.Ducros, and G.J.Davies (2004).
Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules.
  Structure, 12, 1177-1187.
PDB codes: 1ux7 1w0n
15010454 V.M.Pires, J.L.Henshaw, J.A.Prates, D.N.Bolam, L.M.Ferreira, C.M.Fontes, B.Henrissat, A.Planas, H.J.Gilbert, and M.Czjzek (2004).
The crystal structure of the family 6 carbohydrate binding module from Cellvibrio mixtus endoglucanase 5a in complex with oligosaccharides reveals two distinct binding sites with different ligand specificities.
  J Biol Chem, 279, 21560-21568.
PDB codes: 1uxx 1uxz 1uy0 1uyx 1uyy 1uyz 1uz0
15490156 Y.Ohta, Y.Hatada, Y.Nogi, Z.Li, S.Ito, and K.Horikoshi (2004).
Cloning, expression, and characterization of a glycoside hydrolase family 86 beta-agarase from a deep-sea Microbulbifer-like isolate.
  Appl Microbiol Biotechnol, 66, 266-275.  
15170112 Y.Ohta, Y.Nogi, M.Miyazaki, Z.Li, Y.Hatada, S.Ito, and K.Horikoshi (2004).
Enzymatic properties and nucleotide and amino acid sequences of a thermostable beta-agarase from the novel marine isolate, JAMB-A94.
  Biosci Biotechnol Biochem, 68, 1073-1081.  
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 codes are shown on the right.