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PDBsum entry 1ece
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Glycosyl hydrolase PDB id
1ece

 

 

 

 

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Contents
Protein chains
358 a.a. *
Ligands
BGC-BGC-BGC-BGC ×2
Waters ×375
* Residue conservation analysis
PDB id:
1ece
Name: Glycosyl hydrolase
Title: Acidothermus cellulolyticus endocellulase e1 catalytic domain in complex with a cellotetraose
Structure: Endocellulase e1. Chain: a, b. Fragment: catalytic domain. Synonym: endo-1,4-beta-d-glucanase. Engineered: yes
Source: Acidothermus cellulolyticus. Organism_taxid: 28049. Gene: pvu i fragment of a.. Expressed in: streptomyces lividans tk24. Expression_system_taxid: 457428. DNA carrying native e1 gene
Resolution:
2.40Å     R-factor:   0.179     R-free:   0.236
Authors: J.Sakon,S.R.Thomas,M.E.Himmel,P.A.Karplus
Key ref: J.Sakon et al. (1996). Crystal structure of thermostable family 5 endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose. Biochemistry, 35, 10648-10660. PubMed id: 8718854 DOI: 10.1021/bi9604439
Date:
04-Apr-96     Release date:   14-Oct-96    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P54583  (GUN1_ACIC1) -  Endoglucanase E1 from Acidothermus cellulolyticus (strain ATCC 43068 / DSM 8971 / 11B)
Seq:
Struc: 		 
Seq:
Struc: 		562 a.a.
358 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.

 

 
DOI no: 10.1021/bi9604439 Biochemistry 35:10648-10660 (1996)
PubMed id: 8718854  
 
 
Crystal structure of thermostable family 5 endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose.
J.Sakon, W.S.Adney, M.E.Himmel, S.R.Thomas, P.A.Karplus.
 
  ABSTRACT  
 
The crystal structure of the catalytic domain of the thermostable endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose has been solved by multiple isomorphous replacement and refined at 2.4 A resolution to an R-factor of 0.18 (Rfree = 0.24). E1cd is a member of the 4/7 superfamily of hydrolases, and as expected, its structure is an (alpha/beta)8 barrel, which constitutes a prototype for family 5-subfamily 1 cellulases. The cellotetraose molecule binds in a manner consistent with the expected Michaelis complex for the glycosylation half-reaction and reveals that all eight residues conserved in family 5 enzymes are involved in recognition of the glycosyl group attacked during cleavage. Whereas only three residues are conserved in the whole 4/7 superfamily (the Asn/Glu duo and the Glu from which the name is derived), structural comparisons show that all eight residues conserved in family 5 have functional equivalents in the other 4/7 superfamily members, strengthening the case that mechanistic details are conserved throughout the superfamily. On the basis of the structure, a detailed sequence of physical steps of the cleavage mechanism is proposed. A close approach of two key glutamate residues provides an elegant mechanism for the shift in the pKa of the acid/base for the glycosylation and deglycosylation half-reactions. Finally, purely structural based comparisons are used to show that significant differences exist in structural similarity scores resulting from different methods and suggest that caution should be exercised in interpreting such results in terms of implied evolutional relationships.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21367878 T.Taira, Y.Mahoe, N.Kawamoto, S.Onaga, H.Iwasaki, T.Ohnuma, and T.Fukamizo (2011).
Cloning and characterization of a small family 19 chitinase from moss (Bryum coronatum).
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20039375 J.S.VanderGheynst, F.Rezaei, T.M.Dooley, and A.M.Berry (2010).
Switchgrass leaching requirements for solid-state fermentation by Acidothermus cellulolyticus.
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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
19296197 I.S.Ng, C.W.Li, Y.F.Yeh, P.T.Chen, J.L.Chir, C.H.Ma, S.M.Yu, T.H.Ho, and C.G.Tong (2009).
A novel endo-glucanase from the thermophilic bacterium Geobacillus sp. 70PC53 with high activity and stability over a broad range of temperatures.
  Extremophiles, 13, 425-435.  
19270083 R.D.Barabote, G.Xie, D.H.Leu, P.Normand, A.Necsulea, V.Daubin, C.Médigue, W.S.Adney, X.C.Xu, A.Lapidus, R.E.Parales, C.Detter, P.Pujic, D.Bruce, C.Lavire, J.F.Challacombe, T.S.Brettin, and A.M.Berry (2009).
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.
  Genome Res, 19, 1033-1043.  
  19052378 H.W.Kim, K.Mino, and K.Ishikawa (2008).
Crystallization and preliminary X-ray analysis of endoglucanase from Pyrococcus horikoshii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1169-1171.  
17847089 K.Goyal, and S.C.Mande (2008).
Exploiting 3D structural templates for detection of metal-binding sites in protein structures.
  Proteins, 70, 1206-1218.  
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.  
17072684 H.J.Kang, K.Uegaki, H.Fukada, and K.Ishikawa (2007).
Improvement of the enzymatic activity of the hyperthermophilic cellulase from Pyrococcus horikoshii.
  Extremophiles, 11, 251-256.  
17928686 H.W.Kim, Y.Takagi, Y.Hagihara, and K.Ishikawa (2007).
Analysis of the putative substrate binding region of hyperthermophilic endoglucanase from Pyrococcus horikoshii.
  Biosci Biotechnol Biochem, 71, 2585-2587.  
17222127 M.Y.Galperin (2007).
Using archaeal genomics to fight global warming and clostridia to fight cancer.
  Environ Microbiol, 9, 279-286.  
17661047 S.Costanzo, M.D.Ospina-Giraldo, K.L.Deahl, C.J.Baker, and R.W.Jones (2007).
Alternate intron processing of family 5 endoglucanase transcripts from the genus Phytophthora.
  Curr Genet, 52, 115-123.  
18085462 S.Dhawan, and J.Kaur (2007).
Microbial mannanases: an overview of production and applications.
  Crit Rev Biotechnol, 27, 197-216.  
17244618 Y.Ishibashi, T.Nakasone, M.Kiyohara, Y.Horibata, K.Sakaguchi, A.Hijikata, S.Ichinose, A.Omori, Y.Yasui, A.Imamura, H.Ishida, M.Kiso, N.Okino, and M.Ito (2007).
A novel endoglycoceramidase hydrolyzes oligogalactosylceramides to produce galactooligosaccharides and ceramides.
  J Biol Chem, 282, 11386-11396.  
17905739 Y.Kitago, S.Karita, N.Watanabe, M.Kamiya, T.Aizawa, K.Sakka, and I.Tanaka (2007).
Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum.
  J Biol Chem, 282, 35703-35711.
PDB codes: 2e0p 2e4t 2eex 2ej1 2eo7 2eqd
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.  
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.  
15375673 Y.Kashima, K.Mori, H.Fukada, and K.Ishikawa (2005).
Analysis of the function of a hyperthermophilic endoglucanase from Pyrococcus horikoshii that hydrolyzes crystalline cellulose.
  Extremophiles, 9, 37-43.  
14695284 B.Liu, M.Bartlam, R.Gao, W.Zhou, H.Pang, Y.Liu, Y.Feng, and Z.Rao (2004).
Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii.
  Biophys J, 86, 420-427.
PDB code: 1ude
14660638 J.K.McCarthy, A.Uzelac, D.F.Davis, and D.E.Eveleigh (2004).
Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution.
  J Biol Chem, 279, 11495-11502.  
15280361 R.Conde, R.Cueva, G.Pablo, J.Polaina, and G.Larriba (2004).
A search for hyperglycosylation signals in yeast glycoproteins.
  J Biol Chem, 279, 43789-43798.  
14730348 S.C.Taylor, A.D.Ferguson, J.J.Bergeron, and D.Y.Thomas (2004).
The ER protein folding sensor UDP-glucose glycoprotein-glucosyltransferase modifies substrates distant to local changes in glycoprotein conformation.
  Nat Struct Mol Biol, 11, 128-134.
PDB code: 1h4p
15316858 Y.Ma, Y.Xue, Y.Dou, Z.Xu, W.Tao, and P.Zhou (2004).
Characterization and gene cloning of a novel beta-mannanase from alkaliphilic Bacillus sp. N16-5.
  Extremophiles, 8, 447-454.  
12919323 K.Eckert, and E.Schneider (2003).
A thermoacidophilic endoglucanase (CelB) from Alicyclobacillus acidocaldarius displays high sequence similarity to arabinofuranosidases belonging to family 51 of glycoside hydrolases.
  Eur J Biochem, 270, 3593-3602.  
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
12209002 L.R.Lynd, P.J.Weimer, W.H.van Zyl, and I.S.Pretorius (2002).
Microbial cellulose utilization: fundamentals and biotechnology.
  Microbiol Mol Biol Rev, 66, 506.  
11772658 S.Ando, H.Ishida, Y.Kosugi, and K.Ishikawa (2002).
Hyperthermostable endoglucanase from Pyrococcus horikoshii.
  Appl Environ Microbiol, 68, 430-433.  
16233124 J.Hong, H.Tamaki, S.Akiba, K.Yamamoto, and H.Kumagai (2001).
Cloning of a gene encoding a highly stable endo-beta-1,4-glucanase from Aspergillus niger and its expression in yeast.
  J Biosci Bioeng, 92, 434-441.  
11343795 W.Zhao, E.Confalone, H.J.Breukelman, M.P.Sasso, P.A.Jekel, E.Hodge, A.Furia, and J.J.Beintema (2001).
Ruminant brain ribonucleases: expression and evolution.
  Biochim Biophys Acta, 1547, 95.  
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
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
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.  
  10210191 D.H.Juers, R.E.Huber, and B.W.Matthews (1999).
Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases.
  Protein Sci, 8, 122-136.  
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.  
10409823 L.Lo Leggio, S.Kalogiannis, M.K.Bhat, and R.W.Pickersgill (1999).
High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture.
  Proteins, 36, 295-306.
PDB codes: 1tax 1tix
10490104 Q.Xu, D.Buckley, C.Guan, and H.C.Guo (1999).
Structural insights into the mechanism of intramolecular proteolysis.
  Cell, 98, 651-661.
PDB codes: 9gaa 9gac 9gaf
9852062 A.W.Wong, S.He, J.H.Grubb, W.S.Sly, and S.G.Withers (1998).
Identification of Glu-540 as the catalytic nucleophile of human beta-glucuronidase using electrospray mass spectrometry.
  J Biol Chem, 273, 34057-34062.  
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
9556600 M.Hrmova, E.A.MacGregor, P.Biely, R.J.Stewart, and G.B.Fincher (1998).
Substrate binding and catalytic mechanism of a barley beta-D-Glucosidase/(1,4)-beta-D-glucan exohydrolase.
  J Biol Chem, 273, 11134-11143.  
9761834 M.Scott, R.W.Pickersgill, G.P.Hazlewood, D.Bolam, H.J.Gilbert, and G.W.Harris (1998).
Crystallization and preliminary X-ray diffraction studies of a family 26 endo-beta-1,4 mannanase (ManA) from Pseudomonas fluorescens subspecies cellulosa.
  Acta Crystallogr D Biol Crystallogr, 54, 129-131.  
9731776 V.Notenboom, C.Birsan, M.Nitz, D.R.Rose, R.A.Warren, and S.G.Withers (1998).
Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants.
  Nat Struct Biol, 5, 812-818.
PDB code: 2his
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.  
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
9013549 L.F.Mackenzie, G.S.Brooke, J.F.Cutfield, P.A.Sullivan, and S.G.Withers (1997).
Identification of Glu-330 as the catalytic nucleophile of Candida albicans exo-beta-(1,3)-glucanase.
  J Biol Chem, 272, 3161-3167.  
18576090 M.E.Himmel, P.A.Karplus, J.Sakon, W.S.Adney, J.O.Baker, and S.R.Thomas (1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
  Appl Biochem Biotechnol, 63, 315-325.  
9370370 M.Saloheimo, T.Nakari-Setälä, M.Tenkanen, and M.Penttilä (1997).
cDNA cloning of a Trichoderma reesei cellulase and demonstration of endoglucanase activity by expression in yeast.
  Eur J Biochem, 249, 584-591.  
  9300484 S.Raychaudhuri, F.Younas, P.A.Karplus, C.H.Faerman, and D.R.Ripoll (1997).
Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.
  Protein Sci, 6, 1849-1857.  
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.

 

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