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PDBsum entry 1l1y

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1l1y
Jmol
Contents
Protein chains
(+ 0 more) 642 a.a. *
Ligands
BGC-BGC ×6
Waters ×1595
* Residue conservation analysis
PDB id:
1l1y
Name: Hydrolase
Title: The crystal structure and catalytic mechanism of cellobiohydrolase cels, the major enzymatic component of the clostridium thermocellum cellulosome
Structure: Cellobiohydrolase. Chain: a, b, c, d, e, f. Synonym: cellulase ss, endoglucanase ss. Engineered: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Gene: cels. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PQS)
Resolution:
2.40Å     R-factor:   0.191     R-free:   0.224
Authors: B.G.Guimaraes,H.Souchon,B.L.Lytle,J.H.D.Wu,P.M.Alzari
Key ref:
B.G.Guimarães et al. (2002). The crystal structure and catalytic mechanism of cellobiohydrolase CelS, the major enzymatic component of the Clostridium thermocellum Cellulosome. J Mol Biol, 320, 587-596. PubMed id: 12096911 DOI: 10.1016/S0022-2836(02)00497-7
Date:
20-Feb-02     Release date:   17-Jul-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0C2S5  (GUNS_CLOTM) -  Cellulose 1,4-beta-cellobiosidase (reducing end) CelS
Seq:
Struc:
 
Seq:
Struc:
741 a.a.
642 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.176  - Cellulose 1,4-beta-cellobiosidase (reducing end).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellulose catabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
DOI no: 10.1016/S0022-2836(02)00497-7 J Mol Biol 320:587-596 (2002)
PubMed id: 12096911  
 
 
The crystal structure and catalytic mechanism of cellobiohydrolase CelS, the major enzymatic component of the Clostridium thermocellum Cellulosome.
B.G.Guimarães, H.Souchon, B.L.Lytle, J.H.David Wu, P.M.Alzari.
 
  ABSTRACT  
 
Cellobiohydrolase CelS plays an important role in the cellulosome, an active cellulase system produced by the thermophilic anaerobe Clostridium thermocellum. The structures of the catalytic domain of CelS in complex with substrate (cellohexaose) and product (cellobiose) were determined at 2.5 and 2.4 A resolution, respectively. The protein folds into an (alpha/alpha)(6) barrel with a tunnel-shaped substrate-binding region. The conformation of the loops defining the tunnel is intrinsically stable in the absence of substrate, suggesting a model to account for the processive mode of action of family 48 cellobiohydrolases. Structural comparisons with other (alpha/alpha)(6) barrel glycosidases indicate that CelS and endoglucanase CelA, a sequence-unrelated family 8 glycosidase with a groove-shaped substrate-binding region, use the same catalytic machinery to hydrolyze the glycosidic linkage, despite a low sequence similarity and a different endo/exo mode of action. A remarkable feature of the mechanism is the absence, from CelS, of a carboxylic group acting as the base catalyst. The nearly identical arrangement of substrate and functionally important residues in the two active sites strongly suggests an evolutionary relationship between the cellobiohydrolase and endoglucanase families, which can therefore be classified into a new clan of glycoside hydrolases.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Protein-carbohydrate hydrogen bonding interactions in the CelS-cellohexaose complex. Hydrogen bonds are indicated with broken lines; the corresponding distances are given in Å.
Figure 5.
Figure 5. Structural comparison of family 48 cellobiohydrolase CelS and family 8 endoglucanase CelA. (a) Superposition of the catalytic domains of CelS (green) and CelA (red); bound cellooligomers are shown in CPK mode. (b) Detailed view of the substrate-binding region and the four invariant amino acid residues found in CelS (green) and CelA (red). (c) Amino acid residues and the water nucleophile involved in the catalytic mechanism of CelA and (d) the equivalent view in CelS, including the sugar ring at subsite -1 as seen in CelA (colored in brown). All distances are given in Å.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 587-596) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21291533 R.M.Yennamalli, A.J.Rader, J.D.Wolt, and T.Z.Sen (2011).
Thermostability in endoglucanases is fold-specific.
  BMC Struct Biol, 11, 10.  
20373916 C.M.Fontes, and H.J.Gilbert (2010).
Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates.
  Annu Rev Biochem, 79, 655-681.  
20382819 J.A.Izquierdo, M.V.Sizova, and L.R.Lynd (2010).
Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost.
  Appl Environ Microbiol, 76, 3545-3553.  
20967294 M.Saharay, H.Guo, and J.C.Smith (2010).
Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS.
  PLoS One, 5, e12947.  
19830421 X.Z.Zhang, Z.Zhang, Z.Zhu, N.Sathitsuksanoh, Y.Yang, and Y.H.Zhang (2010).
The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity.
  Appl Microbiol Biotechnol, 86, 525-533.  
19234687 H.Rakotoarivonina, C.Terrie, C.Chambon, E.Forano, and P.Mosoni (2009).
Proteomic identification of CBM37-containing cellulases produced by the rumen cellulolytic bacterium Ruminococcus albus 20 and their putative involvement in bacterial adhesion to cellulose.
  Arch Microbiol, 191, 379-388.  
19193645 T.Ishida, S.Fushinobu, R.Kawai, M.Kitaoka, K.Igarashi, and M.Samejima (2009).
Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.
  J Biol Chem, 284, 10100-10109.
PDB codes: 3eqn 3eqo
17227469 E.Berger, D.Zhang, V.V.Zverlov, and W.H.Schwarz (2007).
Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically.
  FEMS Microbiol Lett, 268, 194-201.  
17459873 M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, and R.Kato (2007).
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.
  J Biol Chem, 282, 18497-18509.
PDB codes: 2eab 2eac 2ead 2eae
17360424 M.Newcomb, C.Y.Chen, and J.H.Wu (2007).
Induction of the celC operon of Clostridium thermocellum by laminaribiose.
  Proc Natl Acad Sci U S A, 104, 3747-3752.  
15755956 A.L.Demain, M.Newcomb, and J.H.Wu (2005).
Cellulase, clostridia, and ethanol.
  Microbiol Mol Biol Rev, 69, 124-154.  
15713668 K.Karaveg, A.Siriwardena, W.Tempel, Z.J.Liu, J.Glushka, B.C.Wang, and K.W.Moremen (2005).
Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control.
  J Biol Chem, 280, 16197-16207.
PDB code: 1x9d
15718242 S.Fushinobu, M.Hidaka, Y.Honda, T.Wakagi, H.Shoun, and M.Kitaoka (2005).
Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125.
  J Biol Chem, 280, 17180-17186.
PDB codes: 1wu4 1wu5 1wu6
  16511021 Y.Honda, S.Fushinobu, M.Hidaka, T.Wakagi, H.Shoun, and M.Kitaoka (2005).
Crystallization and preliminary X-ray analysis of reducing-end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 291-292.  
15604820 L.Hildén, and G.Johansson (2004).
Recent developments on cellulases and carbohydrate-binding modules with cellulose affinity.
  Biotechnol Lett, 26, 1683-1693.  
15236244 M.M.Sánchez, D.C.Irwin, F.I.Pastor, D.B.Wilson, and P.Diaz (2004).
Synergistic activity of Paenibacillus sp. BP-23 cellobiohydrolase Cel48C in association with the contiguous endoglucanase Cel9B and with endo- or exo-acting glucanases from Thermobifida fusca.
  Biotechnol Bioeng, 87, 161-169.  
12823562 M.M.Sánchez, F.I.Pastor, and P.Diaz (2003).
Exo-mode of action of cellobiohydrolase Cel48C from Paenibacillus sp. BP-23. A unique type of cellulase among Bacillales.
  Eur J Biochem, 270, 2913-2919.  
12730163 T.W.Dror, E.Morag, A.Rolider, E.A.Bayer, R.Lamed, and Y.Shoham (2003).
Regulation of the cellulosomal CelS (cel48A) gene of Clostridium thermocellum is growth rate dependent.
  J Bacteriol, 185, 3042-3048.  
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.