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PDBsum entry 1ulo

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protein links
Cellulose degradation PDB id
1ulo
Jmol
Contents
Protein chain
152 a.a. *
* Residue conservation analysis
PDB id:
1ulo
Name: Cellulose degradation
Title: N-terminal cellulose-binding domain from cellulomonas fimi beta-1,4-glucanasE C, nmr, minimized average structure
Structure: EndoglucanasE C. Chain: a. Fragment: n-terminal cellulose-binding domain. Synonym: cenc, endo-1,4-beta-glucanasE C. Engineered: yes
Source: Cellulomonas fimi. Organism_taxid: 1708. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: P.E.Johnson,L.P.Mcintosh
Key ref:
P.E.Johnson et al. (1996). Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy. Biochemistry, 35, 14381-14394. PubMed id: 8916925 DOI: 10.1021/bi961612s
Date:
27-Jul-96     Release date:   01-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P14090  (GUNC_CELFA) -  Endoglucanase C
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1101 a.a.
152 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!
  Biochemical function     hydrolase activity, acting on glycosyl bonds     1 term  

 

 
DOI no: 10.1021/bi961612s Biochemistry 35:14381-14394 (1996)
PubMed id: 8916925  
 
 
Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy.
P.E.Johnson, M.D.Joshi, P.Tomme, D.G.Kilburn, L.P.McIntosh.
 
  ABSTRACT  
 
Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from Cellulomonas fimi 1,4-beta-glucanase CenC (CBDN1). CBDN1 was studied in the presence of saturating concentrations of cellotetraose, but due to spectral overlap, the oligosaccharide was not included in the structure calculations. A total of 1705 interproton nuclear Overhauser effect (NOE), 56 phi, 88 psi, 42 chi 1, 9 chi 2 dihedral angle, and 88 hydrogen-bond restraints were used to calculate 25 final structures. These structures have a rmsd from the average of 0.79 +/- 0.11 A for all backbone atoms excluding disordered termini and 0.44 +/- 0.05 A for residues with regular secondary structures. CBDN1 is composed of 10 beta-strands, folded into two antiparallel beta-sheets with the topology of a jelly-roll beta-sandwich. The strands forming the face of the protein previously determined by chemical shift perturbations to be responsible for cellooligosaccharide binding [Johnson, P. E., Tomme, P., Joshi, M. D., & McIntosh, L. P. (1996) Biochemistry 35, 13895-13906] are shorter than those forming the opposite side of the protein. This results in a 5-stranded binding cleft, containing a central strip of hydrophobic residues that is flanked on both sides by polar hydrogen-bonding groups. The presence of this cleft provides a structural explanation for the unique selectivity of CBDN1 for amorphous cellulose and other soluble oligosaccharides and the lack of binding to crystalline cellulose. The tertiary structure of CBDN1 is strikingly similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other sugar-binding proteins with jelly-roll folds.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20130106 C.A.Dodson, N.Ferguson, T.J.Rutherford, C.M.Johnson, and A.R.Fersht (2010).
Engineering a two-helix bundle protein for folding studies.
  Protein Eng Des Sel, 23, 357-364.
PDB code: 2wqg
18802694 Y.M.Cheng, T.Y.Hong, C.C.Liu, and M.Meng (2009).
Cloning and functional characterization of a complex endo-beta-1,3-glucanase from Paenibacillus sp.
  Appl Microbiol Biotechnol, 81, 1051-1061.  
17554045 C.R.Pigott, and D.J.Ellar (2007).
Role of receptors in Bacillus thuringiensis crystal toxin activity.
  Microbiol Mol Biol Rev, 71, 255-281.  
16826543 A.Roberts, J.G.Pelton, and D.E.Wemmer (2006).
Structural studies of MJ1529, an O6-methylguanine-DNA methyltransferase.
  Magn Reson Chem, 44, S71-S82.
PDB code: 2g7h
16621834 P.Boonserm, M.Mo, C.Angsuthanasombat, and J.Lescar (2006).
Structure of the functional form of the mosquito larvicidal Cry4Aa toxin from Bacillus thuringiensis at a 2.8-angstrom resolution.
  J Bacteriol, 188, 3391-3401.
PDB code: 2c9k
15866877 H.Ichinose, M.Yoshida, T.Kotake, A.Kuno, K.Igarashi, Y.Tsumuraya, M.Samejima, J.Hirabayashi, H.Kobayashi, and S.Kaneko (2005).
An exo-beta-1,3-galactanase having a novel beta-1,3-galactan-binding module from Phanerochaete chrysosporium.
  J Biol Chem, 280, 25820-25829.  
  16233373 C.J.Liu, T.Suzuki, S.Hirata, and K.Kawai (2003).
The processing of high-molecular-weight xylanase (XynE, 110 kDa) from Aeromonas caviae ME-1 to 60-kDa xylanase (XynE60) in Escherichia coli and purification and characterization of XynE60.
  J Biosci Bioeng, 95, 95.  
12833544 D.J.Rigden, and M.J.Jedrzejas (2003).
Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase.
  Proteins, 52, 203-211.  
12486727 M.Roberge, R.N.Lewis, F.Shareck, R.Morosoli, D.Kluepfel, C.Dupont, and R.N.McElhaney (2003).
Differential scanning calorimetric, circular dichroism, and Fourier transform infrared spectroscopic characterization of the thermal unfolding of xylanase A from Streptomyces lividans.
  Proteins, 50, 341-354.  
12511497 T.Arai, R.Araki, A.Tanaka, S.Karita, T.Kimura, K.Sakka, and K.Ohmiya (2003).
Characterization of a cellulase containing a family 30 carbohydrate-binding module (CBM) derived from Clostridium thermocellum CelJ: importance of the CBM to cellulose hydrolysis.
  J Bacteriol, 185, 504-512.  
12191997 B.W.McLean, A.B.Boraston, D.Brouwer, N.Sanaie, C.A.Fyfe, R.A.Warren, D.G.Kilburn, and C.A.Haynes (2002).
Carbohydrate-binding modules recognize fine substructures of cellulose.
  J Biol Chem, 277, 50245-50254.  
11980475 P.J.Simpson, S.J.Jamieson, M.Abou-Hachem, E.N.Karlsson, H.J.Gilbert, O.Holst, and M.P.Williamson (2002).
The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase.
  Biochemistry, 41, 5712-5719.
PDB codes: 1k42 1k45
11371185 A.B.Boraston, A.L.Creagh, M.M.Alam, J.M.Kormos, P.Tomme, C.A.Haynes, R.A.Warren, and D.G.Kilburn (2001).
Binding specificity and thermodynamics of a family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A.
  Biochemistry, 40, 6240-6247.  
11327868 D.N.Bolam, H.Xie, P.White, P.J.Simpson, S.M.Hancock, M.P.Williamson, and H.J.Gilbert (2001).
Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A.
  Biochemistry, 40, 2468-2477.
PDB codes: 1heh 1hej
11478884 H.Xie, H.J.Gilbert, S.J.Charnock, G.J.Davies, M.P.Williamson, P.J.Simpson, S.Raghothama, C.M.Fontes, F.M.Dias, L.M.Ferreira, and D.N.Bolam (2001).
Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding.
  Biochemistry, 40, 9167-9176.
PDB codes: 1h6x 1h6y
11160085 I.A.Kataeva, R.D.Seidel, X.L.Li, and L.G.Ljungdahl (2001).
Properties and mutation analysis of the CelK cellulose-binding domain from the Clostridium thermocellum cellulosome.
  J Bacteriol, 183, 1552-1559.  
  11454740 M.A.Sung, K.Fleming, H.A.Chen, and S.Matthews (2001).
The solution structure of PapGII from uropathogenic Escherichia coli and its recognition of glycolipid receptors.
  EMBO Rep, 2, 621-627.  
  11673472 M.Czjzek, D.N.Bolam, A.Mosbah, J.Allouch, C.M.Fontes, L.M.Ferreira, O.Bornet, V.Zamboni, H.Darbon, N.L.Smith, G.W.Black, B.Henrissat, and H.J.Gilbert (2001).
The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
  J Biol Chem, 276, 48580-48587.
PDB code: 1gmm
11272844 M.K.Ali, H.Hayashi, S.Karita, M.Goto, T.Kimura, K.Sakka, and K.Ohmiya (2001).
Importance of the carbohydrate-binding module of Clostridium stercorarium Xyn10B to xylan hydrolysis.
  Biosci Biotechnol Biochem, 65, 41-47.  
11371186 V.Notenboom, A.B.Boraston, D.G.Kilburn, and D.R.Rose (2001).
Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms.
  Biochemistry, 40, 6248-6256.
PDB codes: 1i82 1i8a 1i8u
10841539 C.D.Mackereth, C.H.Arrowsmith, A.M.Edwards, and L.P.McIntosh (2000).
Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.
  Proc Natl Acad Sci U S A, 97, 6316-6321.
PDB code: 1ef4
10704194 E.Brun, P.E.Johnson, A.L.Creagh, P.Tomme, P.Webster, C.A.Haynes, and L.P.McIntosh (2000).
Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C.
  Biochemistry, 39, 2445-2458.
PDB code: 1cx1
10866795 J.F.Espinosa, J.L.Asensio, J.L.García, J.Laynez, M.Bruix, C.Wright, H.C.Siebert, H.J.Gabius, F.J.Cañada, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.
  Eur J Biochem, 267, 3965-3978.  
10913296 J.Kormos, P.E.Johnson, E.Brun, P.Tomme, L.P.McIntosh, C.A.Haynes, and D.G.Kilburn (2000).
Binding site analysis of cellulose binding domain CBD(N1) from endoglucanse C of Cellulomonas fimi by site-directed mutagenesis.
  Biochemistry, 39, 8844-8852.  
10842338 J.L.Asensio, H.C.Siebert, C.W.von Der Lieth, J.Laynez, M.Bruix, U.M.Soedjanaamadja, J.J.Beintema, F.J.Cañada, H.J.Gabius, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.
  Proteins, 40, 218-236.  
11092922 L.J.Shimon, S.Pagès, A.Belaich, J.P.Belaich, E.A.Bayer, R.Lamed, Y.Shoham, and F.Frolow (2000).
Structure of a family IIIa scaffoldin CBD from the cellulosome of Clostridium cellulolyticum at 2.2 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 1560-1568.
PDB code: 1g43
10809681 M.Hashimoto, T.Ikegami, S.Seino, N.Ohuchi, H.Fukada, J.Sugiyama, M.Shirakawa, and T.Watanabe (2000).
Expression and characterization of the chitin-binding domain of chitinase A1 from Bacillus circulans WL-12.
  J Bacteriol, 182, 3045-3054.  
  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.  
10339551 G.Wang, G.P.Wylie, P.D.Twigg, D.L.Caspar, J.R.Murphy, and T.M.Logan (1999).
Solution structure and peptide binding studies of the C-terminal src homology 3-like domain of the diphtheria toxin repressor protein.
  Proc Natl Acad Sci U S A, 96, 6119-6124.
PDB code: 1bym
10425686 P.J.Simpson, D.N.Bolam, A.Cooper, A.Ciruela, G.P.Hazlewood, H.J.Gilbert, and M.P.Williamson (1999).
A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.
  Structure, 7, 853-864.
PDB codes: 1xbd 2xbd
  10583986 T.Tanaka, S.Fujiwara, S.Nishikori, T.Fukui, M.Takagi, and T.Imanaka (1999).
A unique chitinase with dual active sites and triple substrate binding sites from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
  Appl Environ Microbiol, 65, 5338-5344.  
9521674 A.L.Creagh, J.Koska, P.E.Johnson, P.Tomme, M.D.Joshi, L.P.McIntosh, D.G.Kilburn, and C.A.Haynes (1998).
Stability and oligosaccharide binding of the N1 cellulose-binding domain of Cellulomonas fimi endoglucanase CenC.
  Biochemistry, 37, 3529-3537.  
  9792094 A.Schmidt, A.Schlacher, W.Steiner, H.Schwab, and C.Kratky (1998).
Structure of the xylanase from Penicillium simplicissimum.
  Protein Sci, 7, 2081-2088.
PDB code: 1bg4
9818257 E.A.Bayer, H.Chanzy, R.Lamed, and Y.Shoham (1998).
Cellulose, cellulases and cellulosomes.
  Curr Opin Struct Biol, 8, 548-557.  
9812357 E.N.Karlsson, E.Bartonek-Roxå, and O.Holst (1998).
Evidence for substrate binding of a recombinant thermostable xylanase originating from Rhodothermus marinus.
  FEMS Microbiol Lett, 168, 1-7.  
9707417 M.Caffrey, M.Cai, J.Kaufman, S.J.Stahl, P.T.Wingfield, D.G.Covell, A.M.Gronenborn, and G.M.Clore (1998).
Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41.
  EMBO J, 17, 4572-4584.
PDB codes: 2ezo 2ezp 2ezq 2ezr 2ezs
9737854 P.E.Johnson, A.L.Creagh, E.Brun, K.Joe, P.Tomme, C.A.Haynes, and L.P.McIntosh (1998).
Calcium binding by the N-terminal cellulose-binding domain from Cellulomonas fimi beta-1,4-glucanase CenC.
  Biochemistry, 37, 12772-12781.  
9666333 R.B.Russell, and C.P.Ponting (1998).
Protein fold irregularities that hinder sequence analysis.
  Curr Opin Struct Biol, 8, 364-371.  
  9537359 S.Walter, E.Wellmann, and H.Schrempf (1998).
The cell wall-anchored Streptomyces reticuli avicel-binding protein (AbpS) and its gene.
  J Bacteriol, 180, 1647-1654.  
  9620957 V.V.Zverlov, G.V.Velikodvorskaya, W.H.Schwarz, K.Bronnenmeier, J.Kellermann, and W.L.Staudenbauer (1998).
Multidomain structure and cellulosomal localization of the Clostridium thermocellum cellobiohydrolase CbhA.
  J Bacteriol, 180, 3091-3099.  
  9827993 Y.Gao, K.Kaluarachchi, and D.P.Giedroc (1998).
Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.
  Protein Sci, 7, 2265-2280.
PDB code: 1cl4
9255062 A.Marchler-Bauer, and S.H.Bryant (1997).
A measure of success in fold recognition.
  Trends Biochem Sci, 22, 236-240.  
9195884 K.Sorimachi, M.F.Le Gal-Coëffet, G.Williamson, D.B.Archer, and M.P.Williamson (1997).
Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin.
  Structure, 5, 647-661.
PDB codes: 1ac0 1acz
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 code is shown on the right.