PDBsum entry 6a3h

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Hydrolase PDB id
Protein chain
300 a.a. *
GOL ×8
Waters ×331
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: 2-deoxy-2-fluro-b-d-cellotriosyl/enzyme intermediate complex endoglucanase cel5a from bacillus agaradhearans at 1.6 angs resolution
Structure: Endoglucanase. Chain: a. Fragment: catalytic core domain only. Synonym: cellulase. Engineered: yes. Other_details: this is a complex with 2-deoxy-2-fluorocello covalently linked to the enzymatic nucleophile, glu 228
Source: Bacillus agaradhaerens. Organism_taxid: 76935. Strain: ac13 (ncimb 40482). Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
1.68Å     R-factor:   0.150     R-free:   0.185
Authors: G.J.Davies,A.Varrot,M.Dauter,A.M.Brzozowski,M.Schulein,L.Mac S.G.Withers
Key ref:
G.J.Davies et al. (1998). Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase. Biochemistry, 37, 11707-11713. PubMed id: 9718293 DOI: 10.1021/bi981315i
22-Jul-98     Release date:   24-Jul-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O85465  (GUN5_BACAG) -  Endoglucanase 5A
400 a.a.
300 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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/bi981315i Biochemistry 37:11707-11713 (1998)
PubMed id: 9718293  
Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.
G.J.Davies, L.Mackenzie, A.Varrot, M.Dauter, A.M.Brzozowski, M.Schülein, S.G.Withers.
The enzymatic hydrolysis of O-glycosidic linkages is one of the most diverse and widespread reactions in nature and involves a classic "textbook" enzyme mechanism. A multidisciplinary analysis of a beta-glycoside hydrolase, the Cel5A from Bacillus agaradhaerens, is presented in which the structures of each of the native, substrate, covalent-intermediate, and product complexes have been determined and their interconversions analyzed kinetically, providing unprecedented insights into the mechanism of this enzyme class. Substrate is bound in a distorted 1S3 skew-boat conformation, thereby presenting the anomeric carbon appropriately for nucleophilic attack as well as satisfying the stereoelectronic requirements for an incipient oxocarbenium ion. Leaving group departure results in the trapping of a covalent alpha-glycosyl-enzyme intermediate in which the sugar adopts an undistorted 4C1 conformation. Finally, hydrolysis of this intermediate yields a product complex in which the sugar is bound in a partially disordered mode, consistent with unfavorable interactions and low product affinity.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20127424 D.B.Jordan, and J.D.Braker (2010).
beta-D-Xylosidase from Selenomonas ruminantium: role of glutamate 186 in catalysis revealed by site-directed mutagenesis, alternate substrates, and active-site inhibitor.
  Appl Biochem Biotechnol, 161, 395-410.  
20967294 M.Saharay, H.Guo, and J.C.Smith (2010).
Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS.
  PLoS One, 5, e12947.  
20435641 Y.Takaoka, M.Ohta, A.Takeuchi, K.Miura, M.Matsuo, T.Sakaeda, A.Sugano, and H.Nishio (2010).
Ligand orientation governs conjugation capacity of UDP-glucuronosyltransferase 1A1.
  J Biochem, 148, 25-28.  
19908331 K.Eurich, M.Segawa, S.Toei-Shimizu, and E.Mizoguchi (2009).
Potential role of chitinase 3-like-1 in inflammation-associated carcinogenic changes of epithelial cells.
  World J Gastroenterol, 15, 5249-5259.  
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
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
17728868 A.Scaffidi, K.A.Stubbs, R.J.Dennis, E.J.Taylor, G.J.Davies, D.J.Vocadlo, and R.V.Stick (2007).
A 1-acetamido derivative of 6-epi-valienamine: an inhibitor of a diverse group of beta-N-acetylglucosaminidases.
  Org Biomol Chem, 5, 3013-3019.
PDB code: 2jiw
17766382 J.Dechancie, F.R.Clemente, A.J.Smith, H.Gunaydin, Y.L.Zhao, X.Zhang, and K.N.Houk (2007).
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design.
  Protein Sci, 16, 1851-1866.  
17376777 T.M.Gloster, F.M.Ibatullin, K.Macauley, J.M.Eklöf, S.Roberts, J.P.Turkenburg, M.E.Bjørnvad, P.L.Jørgensen, S.Danielsen, K.S.Johansen, T.V.Borchert, K.S.Wilson, H.Brumer, and G.J.Davies (2007).
Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12.
  J Biol Chem, 282, 19177-19189.
PDB codes: 2jem 2jen 2jep 2jeq
17252125 T.M.Gloster, R.Madsen, and G.J.Davies (2007).
Structural basis for cyclophellitol inhibition of a beta-glucosidase.
  Org Biomol Chem, 5, 444-446.
PDB code: 2jal
16240096 E.Papaleo, P.Fantucci, M.Vai, and L.De Gioia (2006).
Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation.
  J Mol Model, 12, 237-248.  
16628756 T.M.Gloster, R.Madsen, and G.J.Davies (2006).
Dissection of conformationally restricted inhibitors binding to a beta-glucosidase.
  Chembiochem, 7, 738-742.
PDB codes: 2cbu 2cbv
16823793 V.A.Money, N.L.Smith, A.Scaffidi, R.V.Stick, H.J.Gilbert, and G.J.Davies (2006).
Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
  Angew Chem Int Ed Engl, 45, 5136-5140.
PDB codes: 2cip 2cit
16421930 V.Receveur-Bréchot, M.Czjzek, A.Barre, A.Roussel, W.J.Peumans, E.J.Van Damme, and P.Rougé (2006).
Crystal structure at 1.45-A resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome.
  Proteins, 63, 235-242.
PDB code: 2cyg
16260784 X.Biarnés, J.Nieto, A.Planas, and C.Rovira (2006).
Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase. Insight from first principles molecular dynamics simulations.
  J Biol Chem, 281, 1432-1441.  
15501829 A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, and N.C.Strynadka (2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
  J Biol Chem, 280, 2105-2115.
PDB codes: 1xsi 1xsj 1xsk
15987675 E.J.Taylor, A.Goyal, C.I.Guerreiro, J.A.Prates, V.A.Money, N.Ferry, C.Morland, A.Planas, J.A.Macdonald, R.V.Stick, H.J.Gilbert, C.M.Fontes, and G.J.Davies (2005).
How family 26 glycoside hydrolases orchestrate catalysis on different polysaccharides: structure and activity of a Clostridium thermocellum lichenase, CtLic26A.
  J Biol Chem, 280, 32761-32767.
PDB codes: 2bv9 2bvd
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
15840830 R.Bourgault, A.J.Oakley, J.D.Bewley, and M.C.Wilce (2005).
Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.
  Protein Sci, 14, 1233-1241.
PDB code: 1rh9
15355340 C.Carotti, E.Ragni, O.Palomares, T.Fontaine, G.Tedeschi, R.Rodríguez, J.P.Latgé, M.Vai, and L.Popolo (2004).
Characterization of recombinant forms of the yeast Gas1 protein and identification of residues essential for glucanosyltransferase activity and folding.
  Eur J Biochem, 271, 3635-3645.  
14691237 G.Kleiger, E.M.Panina, P.Mallick, and D.Eisenberg (2004).
PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence.
  Protein Sci, 13, 221-229.  
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
14997537 J.K.Choi, B.H.Lee, C.H.Chae, and W.Shin (2004).
Computer modeling of the rhamnogalacturonase-"hairy" pectin complex.
  Proteins, 55, 22-33.  
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
15322773 O.J.Sul, J.H.Kim, S.J.Park, Y.J.Son, B.R.Park, D.K.Chung, C.S.Jeong, and I.S.Han (2004).
Characterization and molecular cloning of a novel endoglucanase from Trichoderma sp. C-4.
  Appl Microbiol Biotechnol, 66, 63-70.  
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
12890686 B.Aguilera, K.Ghauharali-van der Vlugt, M.T.Helmond, J.M.Out, W.E.Donker-Koopman, J.E.Groener, R.G.Boot, G.H.Renkema, G.A.van der Marel, J.H.van Boom, H.S.Overkleeft, and J.M.Aerts (2003).
Transglycosidase activity of chitotriosidase: improved enzymatic assay for the human macrophage chitinase.
  J Biol Chem, 278, 40911-40916.  
12837787 D.Mandelman, A.Belaich, J.P.Belaich, N.Aghajari, H.Driguez, and R.Haser (2003).
X-Ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-oligosaccharides.
  J Bacteriol, 185, 4127-4135.
PDB codes: 1g87 1ga2 1k72 1kfg
14517232 K.Hövel, D.Shallom, K.Niefind, V.Belakhov, G.Shoham, T.Baasov, Y.Shoham, and D.Schomburg (2003).
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
  EMBO J, 22, 4922-4932.
PDB codes: 1pz2 1pz3 1qw8 1qw9
12454501 A.Varrot, T.P.Frandsen, H.Driguez, and G.J.Davies (2002).
Structure of the Humicola insolens cellobiohydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-beta-cellobioside, at 1.9 A.
  Acta Crystallogr D Biol Crystallogr, 58, 2201-2204.
PDB code: 1gz1
12413546 A.Vasella, G.J.Davies, and M.Böhm (2002).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 6, 619-629.  
11914491 S.Khademi, D.Zhang, S.M.Swanson, A.Wartenberg, K.Witte, and E.F.Meyer (2002).
Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride.
  Acta Crystallogr D Biol Crystallogr, 58, 660-667.
PDB codes: 1ks4 1ks5
11900558 T.Kaper, H.H.van Heusden, B.van Loo, A.Vasella, J.van der Oost, and Vos (2002).
Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues.
  Biochemistry, 41, 4147-4155.  
11856334 T.P.Frandsen, M.M.Palcic, and B.Svensson (2002).
Substrate recognition by three family 13 yeast alpha-glucosidases.
  Eur J Biochem, 269, 728-734.  
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
11522797 B.L.Mark, D.J.Vocadlo, D.Zhao, S.Knapp, S.G.Withers, and M.N.James (2001).
Biochemical and structural assessment of the 1-N-azasugar GalNAc-isofagomine as a potent family 20 beta-N-acetylhexosaminidase inhibitor.
  J Biol Chem, 276, 42131-42137.
PDB code: 1jak
11481469 D.M.van Aalten, D.Komander, B.Synstad, S.Gåseidnes, M.G.Peter, and V.G.Eijsink (2001).
Structural insights into the catalytic mechanism of a family 18 exo-chitinase.
  Proc Natl Acad Sci U S A, 98, 8979-8984.
PDB codes: 1e6n 1e6p 1e6r 1e6z
11709165 M.Hrmova, J.N.Varghese, R.De Gori, B.J.Smith, H.Driguez, and G.B.Fincher (2001).
Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.
  Structure, 9, 1005-1016.
PDB codes: 1ieq 1iev 1iew 1iex
11223884 O.D.Schärer, and J.Jiricny (2001).
Recent progress in the biology, chemistry and structural biology of DNA glycosylases.
  Bioessays, 23, 270-281.  
11329289 Y.Hou, D.J.Vocadlo, A.Leung, S.G.Withers, and D.Mahuran (2001).
Characterization of the Glu and Asp residues in the active site of human beta-hexosaminidase B.
  Biochemistry, 40, 2201-2209.  
11150614 A.Planas (2000).
Bacterial 1,3-1,4-beta-glucanases: structure, function and protein engineering.
  Biochim Biophys Acta, 1543, 361-382.  
11006547 C.S.Rye, and S.G.Withers (2000).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 4, 573-580.  
10933800 D.O.Hart, S.He, C.J.Chany, S.G.Withers, P.F.Sims, M.L.Sinnott, and H.Brumer (2000).
Identification of Asp-130 as the catalytic nucleophile in the main alpha-galactosidase from Phanerochaete chrysosporium, a family 27 glycosyl hydrolase.
  Biochemistry, 39, 9826-9836.  
  10752613 G.P.Connelly, S.G.Withers, and L.P.McIntosh (2000).
Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
  Protein Sci, 9, 512-524.  
11025547 L.L.Leggio, J.Jenkins, G.W.Harris, and R.W.Pickersgill (2000).
X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
  Proteins, 41, 362-373.
PDB code: 1e5n
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
10805771 S.S.Parikh, G.Walcher, G.D.Jones, G.Slupphaug, H.E.Krokan, G.M.Blackburn, and J.A.Tainer (2000).
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
  Proc Natl Acad Sci U S A, 97, 5083-5088.
PDB codes: 1emh 1emj
11042447 U.M.Unligil, and J.M.Rini (2000).
Glycosyltransferase structure and mechanism.
  Curr Opin Struct Biol, 10, 510-517.  
11032794 U.M.Unligil, S.Zhou, S.Yuwaraj, M.Sarkar, H.Schachter, and J.M.Rini (2000).
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
  EMBO J, 19, 5269-5280.
PDB codes: 1fo8 1fo9 1foa
10995222 V.Notenboom, S.J.Williams, R.Hoos, S.G.Withers, and D.R.Rose (2000).
Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
  Biochemistry, 39, 11553-11563.
PDB codes: 1fh7 1fh8 1fh9 1fhd
10821697 Y.Hou, D.Vocadlo, S.Withers, and D.Mahuran (2000).
Role of beta Arg211 in the active site of human beta-hexosaminidase B.
  Biochemistry, 39, 6219-6227.  
11080624 Z.Marković-Housley, G.Miglierini, L.Soldatova, P.J.Rizkallah, U.Müller, and T.Schirmer (2000).
Crystal structure of hyaluronidase, a major allergen of bee venom.
  Structure, 8, 1025-1035.
PDB codes: 1fcq 1fcu 1fcv
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
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
10220321 G.Sidhu, S.G.Withers, N.T.Nguyen, L.P.McIntosh, L.Ziser, and G.D.Brayer (1999).
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
  Biochemistry, 38, 5346-5354.
PDB codes: 1bvv 2bvv
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
10508763 J.Jiménez-Barbero, J.L.Asensio, F.J.Cañada, and A.Poveda (1999).
Free and protein-bound carbohydrate structures.
  Curr Opin Struct Biol, 9, 549-555.  
10587432 K.Piotukh, V.Serra, R.Borriss, and A.Planas (1999).
Protein-carbohydrate interactions defining substrate specificity in Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases as dissected by mutational analysis.
  Biochemistry, 38, 16092-16104.  
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.