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PDBsum entry 1cem

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Glycosyltransferase PDB id
1cem
Jmol
Contents
Protein chain
363 a.a. *
Waters ×266
* Residue conservation analysis
PDB id:
1cem
Name: Glycosyltransferase
Title: Endoglucanase a (cela) catalytic core, residues 33-395
Structure: Cellulase cela (1,4-beta-d-glucan- glucanohydrolase). Chain: a. Fragment: catalytic core residues 33-395. Synonym: endo-1,4-beta-glucanase a. Engineered: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Strain: ncib 10682. Gene: cela. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.65Å     R-factor:   0.162     R-free:   0.191
Authors: P.M.Alzari
Key ref:
P.M.Alzari et al. (1996). The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum. Structure, 4, 265-275. PubMed id: 8805535 DOI: 10.1016/S0969-2126(96)00031-7
Date:
04-Dec-95     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
A3DC29  (GUNA_CLOTH) -  Endoglucanase A
Seq:
Struc:
477 a.a.
363 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     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1016/S0969-2126(96)00031-7 Structure 4:265-275 (1996)
PubMed id: 8805535  
 
 
The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum.
P.M.Alzari, H.Souchon, R.Dominguez.
 
  ABSTRACT  
 
BACKGROUND: Cellulases, which catalyze the hydrolysis of glycosidic bonds in cellulose, can be classified into several different protein families. Endoglucanase CelA is a member of glycosyl hydrolase family 8, a family for which no structural information was previously available. RESULTS: The crystal structure of CelA was determined by multiple isomorphous replacement and refined to 1.65 A resolution. The protein folds into a regular (alpha/alpha)6 barrel formed by six inner and six outer alpha helices. Cello-oligosaccharides bind to an acidic cleft containing at least five D-glucosyl-binding subsites (A-E) such that the scissile glycosidic linkage lies between subsites C and D. The strictly conserved residue Glu95, which occupies the center of the substrate-binding cleft and is hydrogen bonded to the glycosidic oxygen, has been assigned the catalytic role of proton donor. CONCLUSIONS: The present analysis provides a basis for modeling homologous family 8 cellulases. The architecture of the active-site cleft, presenting at least five glucosyl-binding subsites, explains why family 8 cellulases cleave cello-oligosaccharide polymers that are at least five D-glycosyl subunits long. Furthermore, the structure of CelA allows comparison with (alpha/alpha)6 barrel glycosidases that are not related in sequence, suggesting a possible, albeit distant, evolutionary relationship between different families of glycosyl hydrolases.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overall view of the (α/α)[6] barrel of endoglucanase CelA. (a) Side view of CelA showing the active-site cleft at the N-terminal end of the inner helices. The 12 α helices forming the barrel involve residues Gln52–Arg70, Ser94–Cys106, Gln110–Lys121, Thr151–Trp168, Tyr176–Cys191, Pro218–Thr228, Arg232–Val247, Tyr282–Phe293, Gln296–Ala310, Ala334–Ala343, Leu350–Ala362 and Tyr372–Ile384 (as defined by PROCHECK [35]). (b) Stereo Cα trace of CelA, viewed along the barrel axis. Amino acid positions are labeled every 20 residues. Figure 2. Overall view of the (α/α)[6] barrel of endoglucanase CelA. (a) Side view of CelA showing the active-site cleft at the N-terminal end of the inner helices. The 12 α helices forming the barrel involve residues Gln52–Arg70, Ser94–Cys106, Gln110–Lys121, Thr151–Trp168, Tyr176–Cys191, Pro218–Thr228, Arg232–Val247, Tyr282–Phe293, Gln296–Ala310, Ala334–Ala343, Leu350–Ala362 and Tyr372–Ile384 (as defined by PROCHECK [[4]35]). (b) Stereo Cα trace of CelA, viewed along the barrel axis. Amino acid positions are labeled every 20 residues.
Figure 4.
Figure 4. Protein–carbohydrate interactions in the CelA–cellobiose complex. (a) Stereoview showing stacking interactions between sugar rings and aromatic amino acid side chains. (b) Schematic diagram of atomic contacts. Hydrogen bonds are indicated with dashed lines, the corresponding distances are given in å. Several water molecules (labeled ‘O[w]’) mediate enzyme-substrate interactions. Figure 4. Protein–carbohydrate interactions in the CelA–cellobiose complex. (a) Stereoview showing stacking interactions between sugar rings and aromatic amino acid side chains. (b) Schematic diagram of atomic contacts. Hydrogen bonds are indicated with dashed lines, the corresponding distances are given in å. Several water molecules (labeled ‘O[w]’) mediate enzyme-substrate interactions.
 
  The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 265-275) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21344678 G.Hai Tran, T.Desmet, M.R.De Groeve, and W.Soetaert (2011).
Probing the active site of cellodextrin phosphorylase from Clostridium stercorarium: Kinetic characterization, ligand docking, and site-directed mutagenesis.
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21291533 R.M.Yennamalli, A.J.Rader, J.D.Wolt, and T.Z.Sen (2011).
Thermostability in endoglucanases is fold-specific.
  BMC Struct Biol, 11, 10.  
20571949 X.Huang, Z.Shao, Y.Hong, L.Lin, C.Li, F.Huang, H.Wang, and Z.Liu (2010).
Cel8H, a novel endoglucanase from the halophilic bacterium Halomonas sp. S66-4: molecular cloning, heterogonous expression, and biochemical characterization.
  J Microbiol, 48, 318-324.  
20676918 Z.L.Yi, and Z.L.Wu (2010).
Mutations from a family-shuffling-library reveal amino acid residues responsible for the thermostability of endoglucanase CelA from Clostridium thermocellum.
  Biotechnol Lett, 32, 1869-1875.  
19517107 D.Isogawa, T.Fukuda, K.Kuroda, H.Kusaoke, H.Kimoto, S.Suye, and M.Ueda (2009).
Demonstration of catalytic proton acceptor of chitosanase from Paenibacillus fukuinensis by comprehensive analysis of mutant library.
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18414797 K.N.Rajnish, G.M.Choudhary, and P.Gunasekaran (2008).
Functional characterization of a putative endoglucanase gene in the genome of Zymomonas mobilis.
  Biotechnol Lett, 30, 1461-1467.  
17520178 Q.Yao, T.Sun, G.Chen, and W.Liu (2007).
Heterologous expression and site-directed mutagenesis of endoglucanase CelA from Clostridium thermocellum.
  Biotechnol Lett, 29, 1243-1247.  
17235516 V.Spiwok, P.Lipovová, T.Skálová, J.Dusková, J.Dohnálek, J.Hasek, N.J.Russell, and B.Králová (2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
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16527981 B.Li, J.P.Yu, J.S.Brunzelle, G.N.Moll, W.A.van der Donk, and S.K.Nair (2006).
Structure and mechanism of the lantibiotic cyclase involved in nisin biosynthesis.
  Science, 311, 1464-1467.
PDB codes: 2g02 2g0d
16532363 C.C.Lee, R.E.Kibblewhite-Accinelli, K.Wagschal, G.H.Robertson, and D.W.Wong (2006).
Cloning and characterization of a cold-active xylanase enzyme from an environmental DNA library.
  Extremophiles, 10, 295-300.  
16804941 Y.Yasutake, S.Kawano, K.Tajima, M.Yao, Y.Satoh, M.Munekata, and I.Tanaka (2006).
Structural characterization of the Acetobacter xylinum endo-beta-1,4-glucanase CMCax required for cellulose biosynthesis.
  Proteins, 64, 1069-1077.
PDB code: 1wzz
15718242 S.Fushinobu, M.Hidaka, Y.Honda, T.Wakagi, H.Shoun, and M.Kitaoka (2005).
Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125.
  J Biol Chem, 280, 17180-17186.
PDB codes: 1wu4 1wu5 1wu6
  16511009 S.Kawano, Y.Yasutake, K.Tajima, Y.Satoh, M.Yao, I.Tanaka, and M.Munekata (2005).
Crystallization and preliminary crystallographic analysis of the cellulose biosynthesis-related protein CMCax from Acetobacter xylinum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 252-254.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
  16511021 Y.Honda, S.Fushinobu, M.Hidaka, T.Wakagi, H.Shoun, and M.Kitaoka (2005).
Crystallization and preliminary X-ray analysis of reducing-end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 291-292.  
15632283 Z.Zhang, S.Kochhar, and M.G.Grigorov (2005).
Descriptor-based protein remote homology identification.
  Protein Sci, 14, 431-444.  
14573597 G.Golan, D.Shallom, A.Teplitsky, G.Zaide, S.Shulami, T.Baasov, V.Stojanoff, A.Thompson, Y.Shoham, and G.Shoham (2004).
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.
  J Biol Chem, 279, 3014-3024.
PDB codes: 1k9d 1k9e 1k9f 1l8n 1mqp 1mqq 1mqr
15214728 J.M.An, W.J.Lim, S.Y.Hong, E.C.Shin, E.J.Kim, Y.K.Kim, S.R.Park, and H.D.Yun (2004).
Cloning and characterization of ce/8A gene from Rhizobium leguminosarum bv. trifolii 1536.
  Lett Appl Microbiol, 38, 296-300.  
15148314 T.Itoh, S.Akao, W.Hashimoto, B.Mikami, and K.Murata (2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
  J Biol Chem, 279, 31804-31812.
PDB code: 1vd5
15502334 Y.Sakihama, W.Adachi, S.Shimizu, T.Sunami, T.Fukazawa, M.Suzuki, R.Yatsunami, S.Nakamura, and A.Takénaka (2004).
Crystallization and preliminary X-ray analyses of the active and the inactive forms of family GH-8 chitosanase with subclass II specificity from Bacillus sp. strain K17.
  Acta Crystallogr D Biol Crystallogr, 60, 2081-2083.  
12475991 F.Van Petegem, T.Collins, M.A.Meuwis, C.Gerday, G.Feller, and J.Van Beeumen (2003).
The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.
  J Biol Chem, 278, 7531-7539.
PDB codes: 1h12 1h13 1h14
12198299 A.Schmidt, A.Gonzalez, R.J.Morris, M.Costabel, P.M.Alzari, and V.S.Lamzin (2002).
Advantages of high-resolution phasing: MAD to atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 58, 1433-1441.
PDB code: 1is9
12351821 F.Mo, R.H.Mathiesen, P.M.Alzari, J.Lescar, and B.Rasmussen (2002).
Physical estimation of triplet phases from two new proteins.
  Acta Crystallogr D Biol Crystallogr, 58, 1780-1786.  
12220178 G.Parsiegla, A.Belaïch, J.P.Belaïch, and R.Haser (2002).
Crystal structure of the cellulase Cel9M enlightens structure/function relationships of the variable catalytic modules in glycoside hydrolases.
  Biochemistry, 41, 11134-11142.
PDB codes: 1ia6 1ia7
11854270 H.Kimoto, H.Kusaoke, I.Yamamoto, Y.Fujii, T.Onodera, and A.Taketo (2002).
Biochemical and genetic properties of Paenibacillus glycosyl hydrolase having chitosanase activity and discoidin domain.
  J Biol Chem, 277, 14695-14702.  
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.  
12135472 P.H.Liang, T.P.Ko, and A.H.Wang (2002).
Structure, mechanism and function of prenyltransferases.
  Eur J Biochem, 269, 3339-3354.  
11914490 S.Khademi, L.A.Guarino, H.Watanabe, G.Tokuda, and E.F.Meyer (2002).
Structure of an endoglucanase from termite, Nasutitermes takasagoensis.
  Acta Crystallogr D Biol Crystallogr, 58, 653-659.
PDB codes: 1ks8 1ksc 1ksd
12089151 T.Collins, M.A.Meuwis, I.Stals, M.Claeyssens, G.Feller, and C.Gerday (2002).
A novel family 8 xylanase, functional and physicochemical characterization.
  J Biol Chem, 277, 35133-35139.  
10675327 F.Vallée, F.Lipari, P.Yip, B.Sleno, A.Herscovics, and P.L.Howell (2000).
Crystal structure of a class I alpha1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control.
  EMBO J, 19, 581-588.
PDB code: 1dl2
10985769 G.Parsiegla, C.Reverbel-Leroy, C.Tardif, J.P.Belaich, H.Driguez, and R.Haser (2000).
Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
  Biochemistry, 39, 11238-11246.
PDB codes: 1f9d 1f9o 1fae 1fbo 1fbw
10745007 H.Zhang, M.C.Seabra, and J.Deisenhofer (2000).
Crystal structure of Rab geranylgeranyltransferase at 2.0 A resolution.
  Structure, 8, 241-251.
PDB code: 1dce
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.  
10391926 S.Kawaminami, H.Takahashi, S.Ito, Y.Arata, and I.Shimada (1999).
A multinuclear NMR study of the active site of an endoglucanase from a strain of Bacillus. Use of Trp residues as structural probes.
  J Biol Chem, 274, 19823-19828.  
9596584 B.Nagar, R.G.Jones, R.J.Diefenbach, D.E.Isenman, and J.M.Rini (1998).
X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2.
  Science, 280, 1277-1281.
PDB code: 1c3d
9755156 G.Parsiegla, M.Juy, C.Reverbel-Leroy, C.Tardif, J.P.Belaïch, H.Driguez, and R.Haser (1998).
The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 A resolution.
  EMBO J, 17, 5551-5562.
PDB code: 1fce
9521693 H.P.Fierobe, E.Mirgorodskaya, K.A.McGuire, P.Roepstorff, B.Svensson, and A.J.Clarke (1998).
Restoration of catalytic activity beyond wild-type level in glucoamylase from Aspergillus awamori by oxidation of the Glu400-->Cys catalytic-base mutant to cysteinesulfinic acid.
  Biochemistry, 37, 3743-3752.  
9283074 A.M.Brzozowski, and G.J.Davies (1997).
Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
  Biochemistry, 36, 10837-10845.
PDB code: 7taa
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.  
9434909 H.W.Park, and L.S.Beese (1997).
Protein farnesyltransferase.
  Curr Opin Struct Biol, 7, 873-880.  
9065406 H.W.Park, S.R.Boduluri, J.F.Moomaw, P.J.Casey, and L.S.Beese (1997).
Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution.
  Science, 275, 1800-1804.
PDB code: 1ft1
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
9295270 K.U.Wendt, K.Poralla, and G.E.Schulz (1997).
Structure and function of a squalene cyclase.
  Science, 277, 1811-1815.
PDB code: 1sqc
14538158 M.K.Bhat, and S.Bhat (1997).
Cellulose degrading enzymes and their potential industrial applications.
  Biotechnol Adv, 15, 583-620.  
9365988 P.M.Coutinho, and P.J.Reilly (1997).
Glucoamylase structural, functional, and evolutionary relationships.
  Proteins, 29, 334-347.  
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.