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PDBsum entry 2eng

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Hydrolase (endoglucanase) PDB id
2eng
Jmol
Contents
Protein chain
206 a.a. *
Waters ×244
* Residue conservation analysis
PDB id:
2eng
Name: Hydrolase (endoglucanase)
Title: Endoglucanase v
Structure: Endoglucanase v. Chain: a. Ec: 3.2.1.4
Source: Humicola insolens. Organism_taxid: 34413
Resolution:
1.50Å     R-factor:   0.105     R-free:   0.154
Authors: G.J.Davies,M.Schulein
Key ref:
G.J.Davies et al. (1995). Structures of oligosaccharide-bound forms of the endoglucanase V from Humicola insolens at 1.9 A resolution. Biochemistry, 34, 16210-16220. PubMed id: 8519779 DOI: 10.1021/bi00049a037
Date:
29-Jun-95     Release date:   07-Dec-96    
Supersedes: 1eng
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P43316  (GUN5_HUMIN) -  Endoglucanase-5
Seq:
Struc:
213 a.a.
206 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     metabolic process   4 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1021/bi00049a037 Biochemistry 34:16210-16220 (1995)
PubMed id: 8519779  
 
 
Structures of oligosaccharide-bound forms of the endoglucanase V from Humicola insolens at 1.9 A resolution.
G.J.Davies, S.P.Tolley, B.Henrissat, C.Hjort, M.Schülein.
 
  ABSTRACT  
 
Cellulose, a polymer of beta-1,4-linked glucose residues, is the major polysaccharide component of plant cell walls and the most abundant biopolymer. The underlying mechanisms of the enzymatic degradation of cellulose are of increasing commercial and ecological significance. Endoglucanase V, from the cellulolytic soil hyphomycete Humicola insolens, is an endocellulase, the catalytic core of which consists of 210 amino acids and is known to hydrolyze the beta-1,4 links with inversion of configuration at the anomeric carbon. The major products of cellulose hydrolysis are cellobiose and cellotriose. The crystal structures of the endoglucanase V (EGV) from H. insolens, in native, product (cellobiose), inactive mutant (D10N), and oligosaccharide-bound [(D10N)-cellohexaose] forms, have been determined at resolutions of 1.9 A or better. EGV consists of a six-stranded beta-barrel domain with long interconnecting loops. A 40 A groove exists along the surface of the enzyme, and this contains the catalytic residues, Asp 10 and Asp 121. The two catalytic aspartates sit to either side of the substrate binding groove in an ideal conformation for facilitating cleavage by inversion, their carboxyl groups being separated by approximately 8.5 A. The complex between substrate and inactive mutant reveals excellent density for an oligosaccharide in six of the enzyme's seven substrate binding subsites. No sugar moiety, however, is seen bound to the -1 subsite at the point of cleavage. The geometry of the cleavage site suggests that the enzyme would favor the binding of sugars with an elongated glycosidic bond, as found in the transition state, as opposed to the binding of substrate. The oligosaccharide complexes reveal solvent water suitably placed for participation in a single displacement reaction as first suggested by Koshland in 1953 [Koshland, D. E. (1953) Biol. Rev. 28, 416-436]. A large conformational change takes place upon substrate binding. This "lid flipping" has the effect of increasing the hydrophobic environment of the catalytic proton donor, enclosing the active site at the point of cleavage, and bringing a third aspartate (Asp 114) in close proximity to the substrate. Site-directed mutagenesis of the catalytic residues has been used to confirm their significance in catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22266780 F.Mba Medie, G.J.Davies, M.Drancourt, and B.Henrissat (2012).
Genome analyses highlight the different biological roles of cellulases.
  Nat Rev Microbiol, 10, 227-234.  
20647679 G.Liu, X.Wei, Y.Qin, and Y.Qu (2010).
Characterization of the endoglucanase and glucomannanase activities of a glycoside hydrolase family 45 protein from Penicillium decumbens 114-2.
  J Gen Appl Microbiol, 56, 223-229.  
  20944220 P.J.Turnbaugh, B.Henrissat, and J.I.Gordon (2010).
Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1261-1264.  
20057047 S.Petkun, S.Jindou, L.J.Shimon, S.Rosenheck, E.A.Bayer, R.Lamed, and F.Frolow (2010).
Structure of a family 3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum: structural diversity and implications for carbohydrate binding.
  Acta Crystallogr D Biol Crystallogr, 66, 33-43.
PDB codes: 2wnx 2wo4 2wob
20173066 X.A.Chen, N.Ishida, N.Todaka, R.Nakamura, J.Maruyama, H.Takahashi, and K.Kitamoto (2010).
Promotion of efficient Saccharification of crystalline cellulose by Aspergillus fumigatus Swo1.
  Appl Environ Microbiol, 76, 2556-2561.  
18971341 F.Kerff, A.Amoroso, R.Herman, E.Sauvage, S.Petrella, P.Filée, P.Charlier, B.Joris, A.Tabuchi, N.Nikolaidis, and D.J.Cosgrove (2008).
Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization.
  Proc Natl Acad Sci U S A, 105, 16876-16881.
PDB codes: 2bh0 3d30
18676702 K.Igarashi, T.Ishida, C.Hori, and M.Samejima (2008).
Characterization of an endoglucanase belonging to a new subfamily of glycoside hydrolase family 45 of the basidiomycete Phanerochaete chrysosporium.
  Appl Environ Microbiol, 74, 5628-5634.  
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.  
17952442 R.Guo, M.Ding, S.L.Zhang, G.J.Xu, and F.K.Zhao (2008).
Molecular cloning and characterization of two novel cellulase genes from the mollusc Ampullaria crossean.
  J Comp Physiol [B], 178, 209-215.  
18465027 R.Guo, M.Ding, S.Zhang, G.Xu, and F.Zhao (2008).
Expression and characterization of two secreted His6-tagged endo-beta-1,4-glucanases from the mollusc Ampullaria crossean in Pichia pastoris.
  Acta Biochim Biophys Sin (Shanghai), 40, 419-425.  
17292641 J.Seon Park, J.B.Russell, and D.B.Wilson (2007).
Characterization of a family 45 glycosyl hydrolase from Fibrobacter succinogenes S85.
  Anaerobe, 13, 83-88.  
16984999 N.H.Yennawar, L.C.Li, D.M.Dudzinski, A.Tabuchi, and D.J.Cosgrove (2006).
Crystal structure and activities of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize.
  Proc Natl Acad Sci U S A, 103, 14664-14671.
PDB code: 2hcz
16685709 S.Pyrpassopoulos, M.Vlassi, A.Tsortos, Y.Papanikolau, K.Petratos, C.E.Vorgias, and G.Nounesis (2006).
Equilibrium heat-induced denaturation of chitinase 40 from Streptomyces thermoviolaceus.
  Proteins, 64, 513-523.  
16356276 J.Sampedro, and D.J.Cosgrove (2005).
The expansin superfamily.
  Genome Biol, 6, 242.  
15272305 A.Buschiazzo, J.E.Ugalde, M.E.Guerin, W.Shepard, R.A.Ugalde, and P.M.Alzari (2004).
Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation.
  EMBO J, 23, 3196-3205.
PDB codes: 1rzu 1rzv
15073875 D.B.Wilson (2004).
Studies of Thermobifida fusca plant cell wall degrading enzymes.
  Chem Rec, 4, 72-82.  
15574890 G.R.LeCleir, A.Buchan, and J.T.Hollibaugh (2004).
Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions.
  Appl Environ Microbiol, 70, 6977-6983.  
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
12657806 J.Valjakka, and J.Rouvinen (2003).
Structure of 20K endoglucanase from Melanocarpus albomyces at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 765-768.
PDB code: 1l8f
11754346 J.Karlsson, D.Momcilovic, B.Wittgren, M.Schülein, F.Tjerneld, and G.Brinkmalm (2002).
Enzymatic degradation of carboxymethyl cellulose hydrolyzed by the endoglucanases Cel5A, Cel7B, and Cel45A from Humicola insolens and Cel7B, Cel12A and Cel45Acore from Trichoderma reesei.
  Biopolymers, 63, 32-40.  
11807269 M.Hirvonen, and A.C.Papageorgiou (2002).
Crystallization and preliminary crystallographic analysis of a family 45 endoglucanase from the thermophilic fungus Melanocarpus albomyces.
  Acta Crystallogr D Biol Crystallogr, 58, 336-338.  
12199698 M.Saloheimo, M.Paloheimo, S.Hakola, J.Pere, B.Swanson, E.Nyyssönen, A.Bhatia, M.Ward, and M.Penttilä (2002).
Swollenin, a Trichoderma reesei protein with sequence similarity to the plant expansins, exhibits disruption activity on cellulosic materials.
  Eur J Biochem, 269, 4202-4211.  
11921222 V.Boyer, S.Fort, T.P.Frandsen, M.Schülein, S.Cottaz, and H.Driguez (2002).
Chemoenzymatic synthesis of a bifunctionalized cellohexaoside as a specific substrate for the sensitive assay of cellulase by fluorescence quenching.
  Chemistry, 8, 1389-1394.  
11135204 C.Boisset, C.Pétrequin, H.Chanzy, B.Henrissat, and M.Schülein (2001).
Optimized mixtures of recombinant Humicola insolens cellulases for the biodegradation of crystalline cellulose.
  Biotechnol Bioeng, 72, 339-345.  
11828460 S.Fort, A.Varrot, M.Schülein, S.Cottaz, H.Driguez, and G.J.Davies (2001).
Mixed-linkage cellooligosaccharides: a new class of glycoside hydrolase inhibitors.
  Chembiochem, 2, 319-325.
PDB code: 1e5j
10742225 C.Boisset, C.Fraschini, M.Schülein, B.Henrissat, and H.Chanzy (2000).
Imaging the enzymatic digestion of bacterial cellulose ribbons reveals the endo character of the cellobiohydrolase Cel6A from Humicola insolens and its mode of synergy with cellobiohydrolase Cel7A.
  Appl Environ Microbiol, 66, 1444-1452.  
10679451 D.J.Cosgrove, and D.J.Cosgrove (2000).
New genes and new biological roles for expansins.
  Curr Opin Plant Biol, 3, 73-78.  
10923796 F.Nakatani, T.Kawaguchi, G.Takada, J.I.Sumitani, Y.Moriyama, and M.Arai (2000).
Cloning and sequencing of an endoglucanase gene from Scopulariopsis brevicaulis TOF-1212, and its expression in Saccharomyces cerevisiae.
  Biosci Biotechnol Biochem, 64, 1238-1246.  
10974122 R.Maheshwari, G.Bharadwaj, and M.K.Bhat (2000).
Thermophilic fungi: their physiology and enzymes.
  Microbiol Mol Biol Rev, 64, 461-488.  
11541953 D.J.Cosgrove, and D.J.Cosgrove (1999).
Enzymes and other agents that enhance cell wall extensibility.
  Annu Rev Plant Physiol Plant Mol Biol, 50, 391-417.  
10424462 F.Attanasio, M.Bruschi, G.Candiano, R.Galletto, L.Musante, M.Schülein, and G.Rialdi (1999).
Analytical titration curves of glycosyl hydrolase Cel45 by combined isoelectric focusing-electrophoresis.
  Electrophoresis, 20, 1403-1411.  
9894008 F.Lipari, and A.Herscovics (1999).
Calcium binding to the class I alpha-1,2-mannosidase from Saccharomyces cerevisiae occurs outside the EF hand motif.
  Biochemistry, 38, 1111-1118.  
10469642 K.A.Watson, C.McCleverty, S.Geremia, S.Cottaz, H.Driguez, and L.N.Johnson (1999).
Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question.
  EMBO J, 18, 4619-4632.
PDB codes: 1e4o 1qm5
9652138 H.Dalbøge, and L.Lange (1998).
Using molecular techniques to identify new microbial biocatalysts.
  Trends Biotechnol, 16, 265-272.  
9283074 A.M.Brzozowski, and G.J.Davies (1997).
Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
  Biochemistry, 36, 10837-10845.
PDB code: 7taa
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
9334746 J.Sakon, D.Irwin, D.B.Wilson, and P.A.Karplus (1997).
Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca.
  Nat Struct Biol, 4, 810-818.
PDB codes: 1js4 1tf4 3tf4 4tf4
9145112 M.O'Reilly, K.A.Watson, R.Schinzel, D.Palm, and L.N.Johnson (1997).
Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase.
  Nat Struct Biol, 4, 405-412.
PDB code: 1ahp
8952478 G.Sulzenbacher, H.Driguez, B.Henrissat, M.Schülein, and G.J.Davies (1996).
Structure of the Fusarium oxysporum endoglucanase I with a nonhydrolyzable substrate analogue: substrate distortion gives rise to the preferred axial orientation for the leaving group.
  Biochemistry, 35, 15280-15287.
PDB code: 1ovw
8718854 J.Sakon, W.S.Adney, M.E.Himmel, S.R.Thomas, and P.A.Karplus (1996).
Crystal structure of thermostable family 5 endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose.
  Biochemistry, 35, 10648-10660.
PDB code: 1ece
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.