spacer
spacer

PDBsum entry 1j84

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
1j84
Jmol
Contents
Protein chain
179 a.a. *
Ligands
BGC-BGC-BGC-BGC
Metals
_CA
Waters ×156
* Residue conservation analysis
PDB id:
1j84
Name: Hydrolase
Title: Structure of fam17 carbohydrate binding module from clostridium cellulovorans with bound cellotetraose
Structure: Endo-1,4-beta glucanase engf. Chain: a. Engineered: yes
Source: Clostridium cellulovorans. Organism_taxid: 1493. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.02Å     R-factor:   0.225     R-free:   0.264
Authors: V.Notenboom,A.B.Boraston,P.Chiu,A.C.J.Freelove,D.G.Kilburn, D.R.Rose
Key ref:
V.Notenboom et al. (2001). Recognition of cello-oligosaccharides by a family 17 carbohydrate-binding module: an X-ray crystallographic, thermodynamic and mutagenic study. J Mol Biol, 314, 797-806. PubMed id: 11733998 DOI: 10.1006/jmbi.2001.5153
Date:
20-May-01     Release date:   12-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P94622  (P94622_CLOCL) -  Endo-1,4-beta glucanase EngF
Seq:
Struc:
 
Seq:
Struc:
557 a.a.
179 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biological process     cellulose catabolic process   1 term 
  Biochemical function     cellulase activity     1 term  

 

 
DOI no: 10.1006/jmbi.2001.5153 J Mol Biol 314:797-806 (2001)
PubMed id: 11733998  
 
 
Recognition of cello-oligosaccharides by a family 17 carbohydrate-binding module: an X-ray crystallographic, thermodynamic and mutagenic study.
V.Notenboom, A.B.Boraston, P.Chiu, A.C.Freelove, D.G.Kilburn, D.R.Rose.
 
  ABSTRACT  
 
The crystal structure of the Clostridium cellulovorans carbohydrate-binding module (CBM) belonging to family 17 has been solved to 1.7 A resolution by multiple anomalous dispersion methods. CBM17 binds to non-crystalline cellulose and soluble beta-1,4-glucans, with a minimal binding requirement of cellotriose and optimal affinity for cellohexaose. The crystal structure of CBM17 complexed with cellotetraose solved at 2.0 A resolution revealed that binding occurs in a cleft on the surface of the molecule involving two tryptophan residues and several charged amino acids. Thermodynamic binding studies and alanine scanning mutagenesis in combination with the cellotetraose complex structure allowed the mapping of the CBM17 binding cleft. In contrast to the binding groove characteristic of family 4 CBMs, family 17 CBMs appear to have a very shallow binding cleft that may be more accessible to cellulose chains in non-crystalline cellulose than the deeper binding clefts of family 4 CBMs. The structural differences in these two modules may reflect non-overlapping binding niches on cellulose surfaces.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Ribbon representation of the 3D structure of CBM17; depicted in gold is the cellotetraose moiety as observed in the crystal structure. Residues that were predicted to form interactions with the ligand by alanine scanning mutagenesis are shown as ball and stick.
Figure 2.
Figure 2. Cartoon representation of ligand interactions in the binding cleft of CBM17. Green broken lines depict hydrogen bonds (lengths in Å). Orange flares around atoms represent hydrophobic contacts between ligand and protein.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 797-806) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19389758 I.A.Dvortsov, N.A.Lunina, L.A.Chekanovskaya, W.H.Schwarz, V.V.Zverlov, and G.A.Velikodvorskaya (2009).
Carbohydrate-binding properties of a separately folding protein module from {beta}-1,3-glucanase Lic16A of Clostridium thermocellum.
  Microbiology, 155, 2442-2449.  
19420681 Y.Araki, S.Karita, A.Tanaka, M.Kondo, and M.Goto (2009).
Characterization of family 17 and family 28 carbohydrate-binding modules from Clostridium josui Cel5A.
  Biosci Biotechnol Biochem, 73, 1028-1032.  
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.  
18566914 B.Nocek, L.Bigelow, J.Abdullah, and A.Joachimiak (2008).
Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module.
  J Struct Funct Genomics, 9, 1-6.
PDB code: 2a5z
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
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.  
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
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.  
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
15292273 A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
  J Biol Chem, 279, 44907-44914.
PDB codes: 1wd3 1wd4
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.  
12964193 A.Laederach, and P.J.Reilly (2003).
Specific empirical free energy function for automated docking of carbohydrates to proteins.
  J Comput Chem, 24, 1748-1757.  
12729009 K.Sakka, M.Nakanishi, M.Sogabe, T.Arai, H.Ohara, A.Tanaka, T.Kimura, and K.Ohmiya (2003).
Isothermal titration calorimetric studies on the binding of a family 6 carbohydrate-binding module of Clostridium thermocellum xynA with xlylooligosaccharides.
  Biosci Biotechnol Biochem, 67, 406-409.  
12511497 T.Arai, R.Araki, A.Tanaka, S.Karita, T.Kimura, K.Sakka, and K.Ohmiya (2003).
Characterization of a cellulase containing a family 30 carbohydrate-binding module (CBM) derived from Clostridium thermocellum CelJ: importance of the CBM to cellulose hydrolysis.
  J Bacteriol, 185, 504-512.  
12191997 B.W.McLean, A.B.Boraston, D.Brouwer, N.Sanaie, C.A.Fyfe, R.A.Warren, D.G.Kilburn, and C.A.Haynes (2002).
Carbohydrate-binding modules recognize fine substructures of cellulose.
  J Biol Chem, 277, 50245-50254.  
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.