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PDBsum entry 1gu3

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protein ligands links
Carbohydrate-binding module PDB id
1gu3
Jmol
Contents
Protein chain
142 a.a. *
Ligands
BGC-BGC-BGC-BGC-
BGC
Waters ×89
* Residue conservation analysis
PDB id:
1gu3
Name: Carbohydrate-binding module
Title: Cbm4 structure and function
Structure: EndoglucanasE C. Chain: a. Fragment: carbohydrate binding module family 4, residues 1-149. Synonym: endo-1,4-beta-glucanase, cellulasE C, cellulase 9b. Engineered: yes
Source: Cellulomonas fimi. Organism_taxid: 1708. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: carbohydrate binding module of cellulase 9b from cellulomonas fimi
Biol. unit: Dimer (from PDB file)
Resolution:
2.3Å     R-factor:   0.217     R-free:   0.257
Authors: D.Nurizzo,V.Notenboom,G.J.Davies
Key ref:
A.B.Boraston et al. (2002). Differential oligosaccharide recognition by evolutionarily-related beta-1,4 and beta-1,3 glucan-binding modules. J Mol Biol, 319, 1143-1156. PubMed id: 12079353 DOI: 10.1016/S0022-2836(02)00374-1
Date:
22-Jan-02     Release date:   26-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P14090  (GUNC_CELFA) -  Endoglucanase C
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1101 a.a.
142 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.4  - Cellulase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     hydrolase activity, acting on glycosyl bonds     1 term  

 

 
DOI no: 10.1016/S0022-2836(02)00374-1 J Mol Biol 319:1143-1156 (2002)
PubMed id: 12079353  
 
 
Differential oligosaccharide recognition by evolutionarily-related beta-1,4 and beta-1,3 glucan-binding modules.
A.B.Boraston, D.Nurizzo, V.Notenboom, V.Ducros, D.R.Rose, D.G.Kilburn, G.J.Davies.
 
  ABSTRACT  
 
Enzymes active on complex carbohydrate polymers frequently have modular structures in which a catalytic domain is appended to one or more carbohydrate-binding modules (CBMs). Although CBMs have been classified into a number of families based upon sequence, many closely related CBMs are specific for different polysaccharides. In order to provide a structural rationale for the recognition of different polysaccharides by CBMs displaying a conserved fold, we have studied the thermodynamics of binding and three-dimensional structures of the related family 4 CBMs from Cellulomonas fimi Cel9B and Thermotoga maritima Lam16A in complex with their ligands, beta-1,4 and beta-1,3 linked gluco-oligosaccharides, respectively. These two CBMs use a structurally conserved constellation of aromatic and polar amino acid side-chains that interact with sugars in two of the five binding subsites. Differences in the length and conformation of loops in non-conserved regions create binding-site topographies that complement the known solution conformations of their respective ligands. Thermodynamics interpreted in the light of structural information highlights the differential role of water in the interaction of these CBMs with their respective oligosaccharide ligands.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overlap of the observed oligosaccharide conformations for the b-1,4 and b-1,3 glucan chains on (a) CfCBM4-1 and (b) TmCBM4-2 (b;ue) with the solution conformations for these ligands (green).[31. and 37.] Only the five sugar units of laminarihexoase making interactions with TmCBM4-2 are shown.
Figure 4.
Figure 4. A schematic showing (a) the CfCBM4-1-cellopentaose interactions and (b) TmCBM4-2-laminariheptaose interactions. Sugar units that are structurally-equivalent are shown in red and blue.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 319, 1143-1156) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21307569 M.Kitami, T.Kadotani, K.Nakanishi, S.Atsumi, S.Higurashi, T.Ishizaka, A.Watanabe, and R.Sato (2011).
Bacillus thuringiensis Cry toxins bound specifically to various proteins via domain III, which had a galactose-binding domain-like fold.
  Biosci Biotechnol Biochem, 75, 305-312.  
19908036 D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.
  Appl Microbiol Biotechnol, 85, 1241-1249.  
20553556 F.Vincent, A.Round, A.Reynaud, C.Bordi, A.Filloux, and Y.Bourne (2010).
Distinct oligomeric forms of the Pseudomonas aeruginosa RetS sensor domain modulate accessibility to the ligand binding site.
  Environ Microbiol, 12, 1775-1786.
PDB code: 2xbz
20939100 S.Kalkhof, S.Haehn, M.Paulsson, N.Smyth, J.Meiler, and A.Sinz (2010).
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking.
  Proteins, 78, 3409-3427.  
20875088 W.M.Patrick, Y.Nakatani, S.M.Cutfield, M.L.Sharpe, R.J.Ramsay, and J.F.Cutfield (2010).
Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance.
  FEBS J, 277, 4549-4561.
PDB codes: 2pc8 2pf0 3n9k 3o6a
19257855 E.A.Chavelas, and E.García-Hernández (2009).
Heat capacity changes in carbohydrates and protein-carbohydrate complexes.
  Biochem J, 420, 239-247.  
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
19116695 R.E.Nordon, S.J.Craig, and F.C.Foong (2009).
Molecular engineering of the cellulosome complex for affinity and bioenergy applications.
  Biotechnol Lett, 31, 465-476.  
18802694 Y.M.Cheng, T.Y.Hong, C.C.Liu, and M.Meng (2009).
Cloning and functional characterization of a complex endo-beta-1,3-glucanase from Paenibacillus sp.
  Appl Microbiol Biotechnol, 81, 1051-1061.  
18422658 A.Viegas, N.F.Brás, N.M.Cerqueira, P.A.Fernandes, J.A.Prates, C.M.Fontes, M.Bruix, M.J.Romão, A.L.Carvalho, M.J.Ramos, A.L.Macedo, and E.J.Cabrita (2008).
Molecular determinants of ligand specificity in family 11 carbohydrate binding modules: an NMR, X-ray crystallography and computational chemistry approach.
  FEBS J, 275, 2524-2535.  
18025086 B.Bae, S.Ohene-Adjei, S.Kocherginskaya, R.I.Mackie, M.A.Spies, I.K.Cann, and S.K.Nair (2008).
Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA.
  J Biol Chem, 283, 12415-12425.
PDB codes: 2zew 2zex 2zey 2zez
18292090 K.J.Gregg, R.Finn, D.W.Abbott, and A.B.Boraston (2008).
Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.
  J Biol Chem, 283, 12604-12613.
PDB codes: 2vmg 2vmh 2vmi 2vng 2vno 2vnr
18663584 L.C.Tsai, Y.N.Chen, and L.F.Shyur (2008).
Structural modeling of glucanase-substrate complexes suggests a conserved tyrosine is involved in carbohydrate recognition in plant 1,3-1,4-beta-D-glucanases.
  J Comput Aided Mol Des, 22, 915-923.  
18784084 M.E.Caines, H.Zhu, M.Vuckovic, L.M.Willis, S.G.Withers, W.W.Wakarchuk, and N.C.Strynadka (2008).
The Structural Basis for T-antigen Hydrolysis by Streptococcus pneumoniae: A TARGET FOR STRUCTURE-BASED VACCINE DESIGN.
  J Biol Chem, 283, 31279-31283.
PDB code: 3ecq
17554045 C.R.Pigott, and D.J.Ellar (2007).
Role of receptors in Bacillus thuringiensis crystal toxin activity.
  Microbiol Mol Biol Rev, 71, 255-281.  
17690769 E.C.Stanca-Kaposta, D.P.Gamblin, J.Screen, B.Liu, L.C.Snoek, B.G.Davis, and J.P.Simons (2007).
Carbohydrate molecular recognition: a spectroscopic investigation of carbohydrate-aromatic interactions.
  Phys Chem Chem Phys, 9, 4444-4451.  
16230347 A.B.Boraston, M.Healey, J.Klassen, E.Ficko-Blean, A.Lammerts van Bueren, and V.Law (2006).
A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition.
  J Biol Chem, 281, 587-598.
PDB codes: 2c3g 2c3h 2c3v 2c3w 2c3x
16456543 A.R.Aricescu, W.C.Hon, C.Siebold, W.Lu, P.A.van der Merwe, and E.Y.Jones (2006).
Molecular analysis of receptor protein tyrosine phosphatase mu-mediated cell adhesion.
  EMBO J, 25, 701-712.
PDB code: 2c9a
16844685 A.W.Blake, L.McCartney, J.E.Flint, D.N.Bolam, A.B.Boraston, H.J.Gilbert, and J.P.Knox (2006).
Understanding the biological rationale for the diversity of cellulose-directed carbohydrate-binding modules in prokaryotic enzymes.
  J Biol Chem, 281, 29321-29329.  
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
16537424 L.McCartney, A.W.Blake, J.Flint, D.N.Bolam, A.B.Boraston, H.J.Gilbert, and J.P.Knox (2006).
Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules.
  Proc Natl Acad Sci U S A, 103, 4765-4770.  
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.  
16787095 S.P.Kawatkar, D.A.Kuntz, R.J.Woods, D.R.Rose, and G.J.Boons (2006).
Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions.
  J Am Chem Soc, 128, 8310-8319.
PDB codes: 2f7o 2f7p
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
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
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.  
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
12427734 A.B.Boraston, E.Kwan, P.Chiu, R.A.Warren, and D.G.Kilburn (2003).
Recognition and hydrolysis of noncrystalline cellulose.
  J Biol Chem, 278, 6120-6127.  
12842048 A.Varrot, T.P.Frandsen, I.von Ossowski, V.Boyer, S.Cottaz, H.Driguez, M.Schülein, and G.J.Davies (2003).
Structural basis for ligand binding and processivity in cellobiohydrolase Cel6A from Humicola insolens.
  Structure, 11, 855-864.
PDB codes: 1oc5 1oc6 1oc7 1ocb 1ocj
12831897 D.Shallom, and Y.Shoham (2003).
Microbial hemicellulases.
  Curr Opin Microbiol, 6, 219-228.  
12391332 S.J.Charnock, D.N.Bolam, D.Nurizzo, L.Szabó, V.A.McKie, H.J.Gilbert, and G.J.Davies (2002).
Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose.
  Proc Natl Acad Sci U S A, 99, 14077-14082.
PDB codes: 1gwk 1gwl 1gwm
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.