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PDBsum entry 1dym

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Hydrolase PDB id
1dym
Jmol
Contents
Protein chain
398 a.a. *
Ligands
NAG ×2
Waters ×595
* Residue conservation analysis
PDB id:
1dym
Name: Hydrolase
Title: Humicola insolens endocellulase cel7b (eg 1) e197a mutant
Structure: Endoglucanase i. Chain: a. Synonym: cellulase, family 7 endoglucanase, endo-1,4-beta-glucanase. Engineered: yes. Mutation: yes. Other_details: pyroglutamate post-translational modification at residue 1, n-linked n-acetylglucosamine on residue asns 89 and 247
Source: Humicola insolens. Organism_taxid: 34413. Expressed in: aspergillus oryzae. Expression_system_taxid: 5062
Resolution:
1.75Å     R-factor:   0.158     R-free:   0.200
Authors: G.J.Davies,O.Moraz,H.Driguez,M.Schulein
Key ref: L.F.MacKenzie et al. (1998). Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate. Biochem J, 335, 409-416. PubMed id: 9761741
Date:
03-Feb-00     Release date:   04-Feb-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56680  (GUN1_HUMIN) -  Endoglucanase 1
Seq:
Struc:
402 a.a.
398 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
Biochem J 335:409-416 (1998)
PubMed id: 9761741  
 
 
Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate.
L.F.MacKenzie, G.Sulzenbacher, C.Divne, T.A.Jones, H.F.Wöldike, M.Schülein, S.G.Withers, G.J.Davies.
 
  ABSTRACT  
 
Cellulose is the major polysaccharide component of the plant cell wall and the most abundant naturally produced macromolecule on Earth. The enzymic degradation of cellulose, by cellulases, is therefore of great environmental and commercial significance. Cellulases are found in 12 of the glycoside hydrolase families classified according to their amino acid sequence similarities. Endoglucanase I (Cel7B), from the soft-rot fungus Humicola insolens, is a family 7 enzyme. The structure of the native form of Cel7B from H. insolens at 2.2 A resolution has been solved by molecular replacement using the known Trichoderma reesei cellobiohydrolase I [Divne, Ståhlberg, Reinikainen, Ruohonen, Pettersson, Knowles, Teeri and Jones (1994) Science 265, 524-528] structure as the search model. Cel7B catalyses hydrolysis of the beta-1,4 glycosidic linkages in cellulose with net retention of anomeric configuration. The catalytic nucleophile at the active site of Cel7B has been identified as Glu-197 by trapping of a 2-deoxy-2-fluorocellotriosyl enzyme intermediate and identification of the labelled peptide in peptic digests by tandem MS. Site-directed mutagenesis of both Glu-197 and the prospective catalytic acid, Glu-202, results in inactive enzyme, confirming the critical role of these groups for catalysis.
 

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.  
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
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
15130470 M.F.Amaya, A.G.Watts, I.Damager, A.Wehenkel, T.Nguyen, A.Buschiazzo, G.Paris, A.C.Frasch, S.G.Withers, and P.M.Alzari (2004).
Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase.
  Structure, 12, 775-784.
PDB codes: 1s0i 1s0j 1s0k 2ah2
11866092 I.Kwon, K.Ekino, T.Oka, M.Goto, and K.Furukawa (2002).
Effects of amino acid alterations on the transglycosylation reaction of endoglucanase I from Trichoderma viride HK-75.
  Biosci Biotechnol Biochem, 66, 110-116.  
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.  
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
11514661 W.A.Breyer, and B.W.Matthews (2001).
A structural basis for processivity.
  Protein Sci, 10, 1699-1711.  
10974122 R.Maheshwari, G.Bharadwaj, and M.K.Bhat (2000).
Thermophilic fungi: their physiology and enzymes.
  Microbiol Mol Biol Rev, 64, 461-488.  
10413461 A.Varrot, M.Schülein, and G.J.Davies (1999).
Structural changes of the active site tunnel of Humicola insolens cellobiohydrolase, Cel6A, upon oligosaccharide binding.
  Biochemistry, 38, 8884-8891.
PDB code: 2bvw
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.