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PDBsum entry 2a3h

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Endoglucanase PDB id
2a3h
Jmol
Contents
Protein chain
300 a.a. *
Ligands
CBI
Waters ×396
* Residue conservation analysis
PDB id:
2a3h
Name: Endoglucanase
Title: Cellobiose complex of the endoglucanase cel5a from bacillus agaradherans at 2.0 a resolution
Structure: Endoglucanase. Chain: a. Fragment: catalytic core. Synonym: cellulase. Engineered: yes. Other_details: this is a complex with b-d-cellobiose bound in the -2 and -3 sites of the enzyme
Source: Bacillus agaradhaerens. Organism_taxid: 76935. Strain: ac13. Atcc: ncimb 40482. Collection: ncimb 40482. Expressed in: bacillus subtilis. Expression_system_taxid: 1423. Negative strain. System
Resolution:
2.00Å     R-factor:   0.137     R-free:   0.190
Authors: G.J.Davies,A.M.Brzozowski,K.Andersen,M.Schulein
Key ref:
G.J.Davies et al. (1998). Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution. Biochemistry, 37, 1926-1932. PubMed id: 9485319 DOI: 10.1021/bi972162m
Date:
22-Jan-98     Release date:   16-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O85465  (GUN5_BACAG) -  Endoglucanase 5A
Seq:
Struc:
400 a.a.
300 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     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1021/bi972162m Biochemistry 37:1926-1932 (1998)
PubMed id: 9485319  
 
 
Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution.
G.J.Davies, M.Dauter, A.M.Brzozowski, M.E.Bjørnvad, K.V.Andersen, M.Schülein.
 
  ABSTRACT  
 
The enzymatic degradation of cellulose, by cellulases, is not only industrially important in the food, paper, and textile industries but also a potentially useful method for the environmentally friendly recycling of municipal waste. An understanding of the structural and mechanistic requirements for the hydrolysis of the beta-1,4 glycosidic bonds of cellulose is an essential prerequisite for beneficial engineering of cellulases for these processes. Cellulases have been classified into 13 of the 62 glycoside hydrolase families [Henrissat, B., and Bairoch, A. (1996) Biochem J. 316, 695-696]. The structure of the catalytic core of the family 5 endoglucanase, Ce15A, from the alkalophilic Bacillus agaradherans has been solved by multiple isomorphous replacement at 1.6 A resolution. Ce15A has the (alpha/beta)8 barrel structure and signature structural features typical of the grouping of glycoside hydrolase families known as clan GH-A, with the catalytic acid/base Glu 139 and nucleophile Glu 228 on barrel strands beta 4 and beta 7 as expected. In addition to the native enzyme, the 2.0 A resolution structure of the cellobiose-bound form of the enzyme has also been determined. Cellobiose binds preferentially in the -2 and -3 subsites of the enzyme. Kinetic studies on the isolated catalytic core domain of Ce15A, using a series of reduced cellodextrins as substrates, suggest approximately five to six binding sites, consistent with the shape and size of the cleft observed by crystallography.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20803139 C.Liang, Y.Xue, M.Fioroni, F.Rodríguez-Ropero, C.Zhou, U.Schwaneberg, and Y.Ma (2011).
Cloning and characterization of a thermostable and halo-tolerant endoglucanase from Thermoanaerobacter tengcongensis MB4.
  Appl Microbiol Biotechnol, 89, 315-326.  
20875088 W.M.Patrick, Y.Nakatani, S.M.Cutfield, M.L.Sharpe, R.J.Ramsay, and J.F.Cutfield (2010).
Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance.
  FEBS J, 277, 4549-4561.
PDB codes: 2pc8 2pf0 3n9k 3o6a
19543714 H.Schagerlöf, C.Nilsson, L.Gorton, F.Tjerneld, H.Stålbrand, and A.Cohen (2009).
Use of 18O water and ESI-MS detection in subsite characterisation and investigation of the hydrolytic action of an endoglucanase.
  Anal Bioanal Chem, 394, 1977-1984.  
17329247 M.E.Caines, M.D.Vaughan, C.A.Tarling, S.M.Hancock, R.A.Warren, S.G.Withers, and N.C.Strynadka (2007).
Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms.
  J Biol Chem, 282, 14300-14308.
PDB codes: 2osw 2osx 2osy
16710633 K.Hirasawa, K.Uchimura, M.Kashiwa, W.D.Grant, S.Ito, T.Kobayashi, and K.Horikoshi (2006).
Salt-activated endoglucanase of a strain of alkaliphilic Bacillus agaradhaerens.
  Antonie Van Leeuwenhoek, 89, 211-219.  
17010163 N.Beukes, and B.I.Pletschke (2006).
Effect of sulfur-containing compounds on Bacillus cellulosome-associated 'CMCase' and 'Avicelase' activities.
  FEMS Microbiol Lett, 264, 226-231.  
16522010 R.Stern, and M.J.Jedrzejas (2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
  Chem Rev, 106, 818-839.  
16104017 M.J.Jedrzejas, and R.Stern (2005).
Structures of vertebrate hyaluronidases and their unique enzymatic mechanism of hydrolysis.
  Proteins, 61, 227-238.  
15857788 T.Wang, X.Liu, Q.Yu, X.Zhang, Y.Qu, P.Gao, and T.Wang (2005).
Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei.
  Biomol Eng, 22, 89-94.  
15340924 K.B.Murray, W.R.Taylor, and J.M.Thornton (2004).
Toward the detection and validation of repeats in protein structure.
  Proteins, 57, 365-380.  
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
15356002 T.M.Gloster, J.M.Macdonald, C.A.Tarling, R.V.Stick, S.G.Withers, and G.J.Davies (2004).
Structural, thermodynamic, and kinetic analyses of tetrahydrooxazine-derived inhibitors bound to beta-glucosidases.
  J Biol Chem, 279, 49236-49242.
PDB codes: 1w3j 1w3k 1w3l
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
12847093 I.Callebaut, C.Curcio-Morelli, J.P.Mornon, B.Gereben, C.Buettner, S.Huang, B.Castro, T.L.Fonseca, J.W.Harney, P.R.Larsen, and A.C.Bianco (2003).
The iodothyronine selenodeiodinases are thioredoxin-fold family proteins containing a glycoside hydrolase clan GH-A-like structure.
  J Biol Chem, 278, 36887-36896.  
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
11828459 H.Driguez (2001).
Thiooligosaccharides as tools for structural biology.
  Chembiochem, 2, 311-318.  
11222610 J.C.Hurlbert, and J.F.Preston (2001).
Functional characterization of a novel xylanase from a corn strain of Erwinia chrysanthemi.
  J Bacteriol, 183, 2093-2100.  
11679332 M.L.Wu, Y.C.Chuang, J.P.Chen, C.S.Chen, and M.C.Chang (2001).
Identification and characterization of the three chitin-binding domains within the multidomain chitinase Chi92 from Aeromonas hydrophila JP101.
  Appl Environ Microbiol, 67, 5100-5106.  
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
11166997 Y.Hakamada, Y.Hatada, T.Ozawa, K.Ozaki, T.Kobayashi, and S.Ito (2001).
Identification of thermostabilizing residues in a Bacillus alkaline cellulase by construction of chimeras from mesophilic and thermostable enzymes and site-directed mutagenesis.
  FEMS Microbiol Lett, 195, 67-72.  
10666621 E.Sabini, H.Schubert, G.Murshudov, K.S.Wilson, M.Siika-Aho, and M.Penttilä (2000).
The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
  Acta Crystallogr D Biol Crystallogr, 56, 3.
PDB codes: 1qno 1qnp 1qnq 1qnr 1qns
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.  
11018131 T.Y.Wong, L.A.Preston, and N.L.Schiller (2000).
ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.
  Annu Rev Microbiol, 54, 289-340.  
11193393 Y.Hakamada, Y.Hatada, K.Koike, T.Yoshimatsu, S.Kawai, T.Kobayashi, and S.Ito (2000).
Deduced amino acid sequence and possible catalytic residues of a thermostable, alkaline cellulase from an Alkaliphilic bacillus strain.
  Biosci Biotechnol Biochem, 64, 2281-2289.  
10216305 E.Sabini, A.M.Brzozowski, M.Dauter, G.J.Davies, K.S.Wilson, M.Paloheimo, P.Suominen, M.Siika-Aho, and M.Penttilä (1999).
Crystallization and preliminary X-ray crystallographic analysis of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
  Acta Crystallogr D Biol Crystallogr, 55, 1058-1060.  
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
9817845 M.Hilge, S.M.Gloor, W.Rypniewski, O.Sauer, T.D.Heightman, W.Zimmermann, K.Winterhalter, and K.Piontek (1998).
High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
  Structure, 6, 1433-1444.
PDB codes: 1bqc 2man 3man
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.