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PDBsum entry 4ovw

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protein ligands links
Hydrolase PDB id
4ovw
Jmol
Contents
Protein chains
400 a.a. *
Ligands
NAG ×2
IN1 ×2
Waters ×699
* Residue conservation analysis
PDB id:
4ovw
Name: Hydrolase
Title: Endoglucanase i complexed with epoxybutyl cellobiose
Structure: Endoglucanase i. Chain: a, b. Ec: 3.2.1.4
Source: Fusarium oxysporum. Organism_taxid: 5507
Resolution:
2.30Å     R-factor:   0.180     R-free:   0.270
Authors: G.J.Davies,M.Schulein
Key ref:
G.Sulzenbacher et al. (1997). Structure of the endoglucanase I from Fusarium oxysporum: native, cellobiose, and 3,4-epoxybutyl beta-D-cellobioside-inhibited forms, at 2.3 A resolution. Biochemistry, 36, 5902-5911. PubMed id: 9153432 DOI: 10.1021/bi962963+
Date:
06-Oct-97     Release date:   08-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P46237  (GUNC_FUSOX) -  Endoglucanase type C
Seq:
Struc:
429 a.a.
400 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!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1021/bi962963+ Biochemistry 36:5902-5911 (1997)
PubMed id: 9153432  
 
 
Structure of the endoglucanase I from Fusarium oxysporum: native, cellobiose, and 3,4-epoxybutyl beta-D-cellobioside-inhibited forms, at 2.3 A resolution.
G.Sulzenbacher, M.Schülein, G.J.Davies.
 
  ABSTRACT  
 
The mechanisms involved in the enzymatic degradation of cellulose are of great ecological and commercial importance. The breakdown of cellulose by fungal species is performed by a consortium of free enzymes, known as cellobiohydrolases and endoglucanases, which are found in many of the 57 glycosyl hydrolase families. The structure of the endoglucanase I (EG I), found in glycosyl hydrolase family 7, from the thermophilic fungus Fusarium oxysporum has been solved at 2.3 A resolution. In addition to the native enzyme, structures have also been determined with both the affinity label, 3,4-epoxybutyl beta-D-cellobioside, and the reaction product cellobiose. The affinity label is covalently bound, as expected, to the catalytic nucleophile, Glu197, with clear evidence for binding of both the R and S stereoisomers. Cellobiose is found bound to the -2 and -1 subsites of the enzyme. In marked contrast to the structure of EG I with a nonhydrolyzable thiosaccharide analog, which spanned the -2, -1, and +1 subsites and which had a skew-boat conformation for the -1 subsite sugar [Sulzenbacher, G., et al. (1996) Biochemistry 35, 15280-15287], the cellobiose complex shows no pyranoside ring distortion in the -1 subsite, implying that strain is induced primarily by the additional +1 subsite interactions and that the product is found, as expected, in its unstrained conformation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18499583 T.Parkkinen, A.Koivula, J.Vehmaanperä, and J.Rouvinen (2008).
Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding.
  Protein Sci, 17, 1383-1394.
PDB codes: 2rfw 2rfy 2rfz 2rg0
16138313 C.Mulakala, and P.J.Reilly (2005).
Force calculations in automated docking: enzyme-substrate interactions in Fusarium oxysporum Cel7B.
  Proteins, 61, 590-596.  
15853815 J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, and P.Vainiotalo (2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
  FEBS J, 272, 2317-2333.
PDB code: 1xnk
15819888 W.Ubhayasekera, I.G.Muñoz, A.Vasella, J.Ståhlberg, and S.L.Mowbray (2005).
Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors.
  FEBS J, 272, 1952-1964.
PDB codes: 1z3t 1z3v 1z3w
15560790 A.Grassick, P.G.Murray, R.Thompson, C.M.Collins, L.Byrnes, G.Birrane, T.M.Higgins, and M.G.Tuohy (2004).
Three-dimensional structure of a thermostable native cellobiohydrolase, CBH IB, and molecular characterization of the cel7 gene from the filamentous fungus, Talaromyces emersonii.
  Eur J Biochem, 271, 4495-4506.
PDB code: 1q9h
15148317 L.Verdoucq, J.Morinière, D.R.Bevan, A.Esen, A.Vasella, B.Henrissat, and M.Czjze (2004).
Structural determinants of substrate specificity in family 1 beta-glucosidases: novel insights from the crystal structure of sorghum dhurrinase-1, a plant beta-glucosidase with strict specificity, in complex with its natural substrate.
  J Biol Chem, 279, 31796-31803.
PDB codes: 1v02 1v03 1v08
14597633 M.Hrmova, R.De Gori, B.J.Smith, A.Vasella, J.N.Varghese, and G.B.Fincher (2004).
Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
  J Biol Chem, 279, 4970-4980.
PDB code: 1lq2
12595701 A.Varrot, and G.J.Davies (2003).
Direct experimental observation of the hydrogen-bonding network of a glycosidase along its reaction coordinate revealed by atomic resolution analyses of endoglucanase Cel5A.
  Acta Crystallogr D Biol Crystallogr, 59, 447-452.
PDB codes: 1h11 1h2j 1hf6
11679762 A.Varrot, M.Schülein, S.Fruchard, H.Driguez, and G.J.Davies (2001).
Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-alpha-cellopentoside highlights the alternative binding modes targeted by substrate mimics.
  Acta Crystallogr D Biol Crystallogr, 57, 1739-1742.
PDB code: 1h5v
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
11106394 M.Czjzek, M.Cicek, V.Zamboni, D.R.Bevan, B.Henrissat, and A.Esen (2000).
The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.
  Proc Natl Acad Sci U S A, 97, 13555-13560.
PDB codes: 1e4l 1e4n 1e55 1e56
10824094 S.Zhang, D.C.Irwin, and D.B.Wilson (2000).
Site-directed mutation of noncatalytic residues of Thermobifida fusca exocellulase Cel6B.
  Eur J Biochem, 267, 3101-3115.  
10029534 A.Schmidt, G.M.Gübitz, and C.Kratky (1999).
Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant.
  Biochemistry, 38, 2403-2412.
PDB codes: 1b30 1b31 1b3v 1b3w 1b3x 1b3y 1b3z
10381409 E.Sabini, G.Sulzenbacher, M.Dauter, Z.Dauter, P.L.Jørgensen, M.Schülein, C.Dupont, G.J.Davies, and K.S.Wilson (1999).
Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
  Chem Biol, 6, 483-492.
PDB codes: 1h4g 1h4h 1qh6 1qh7
10200171 G.Sulzenbacher, L.F.Mackenzie, K.S.Wilson, S.G.Withers, C.Dupont, and G.J.Davies (1999).
The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.
  Biochemistry, 38, 4826-4833.
PDB code: 2nlr
9888793 M.Muraki, K.Harata, N.Sugita, and K.Sato (1999).
Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand.
  Biochemistry, 38, 540-548.
PDB code: 1re2
9818257 E.A.Bayer, H.Chanzy, R.Lamed, and Y.Shoham (1998).
Cellulose, cellulases and cellulosomes.
  Curr Opin Struct Biol, 8, 548-557.  
9718293 G.J.Davies, L.Mackenzie, A.Varrot, M.Dauter, A.M.Brzozowski, M.Schülein, and S.G.Withers (1998).
Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.
  Biochemistry, 37, 11707-11713.
PDB codes: 3a3h 4a3h 5a3h 6a3h 7a3h
9345622 A.White, and D.R.Rose (1997).
Mechanism of catalysis by retaining beta-glycosyl hydrolases.
  Curr Opin Struct Biol, 7, 645-651.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
9449766 K.Klarskov, K.Piens, J.Ståhlberg, P.B.Høj, J.V.Beeumen, and M.Claeyssens (1997).
Cellobiohydrolase I from Trichoderma reesei: identification of an active-site nucleophile and additional information on sequence including the glycosylation pattern of the core protein.
  Carbohydr Res, 304, 143-154.  
9153431 L.F.Mackenzie, G.J.Davies, M.Schülein, and S.G.Withers (1997).
Identification of the catalytic nucleophile of endoglucanase I from Fusarium oxysporum by mass spectrometry.
  Biochemistry, 36, 5893-5901.  
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.