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PDBsum entry 1aiw
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Cellulose degradation PDB id
1aiw

 

 

 

 

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Contents
Protein chain
62 a.a. *
* Residue conservation analysis
PDB id:
1aiw
Name: Cellulose degradation
Title: Nmr structures of the cellulose-binding domain of the endoglucanase z from erwinia chrysanthemi, 23 structures
Structure: Endoglucanase z. Chain: a. Fragment: c-terminal cellulose-binding domain. Synonym: cbdegz. Engineered: yes. Mutation: yes
Source: Erwinia chrysanthemi. Organism_taxid: 198628. Strain: 3937. Cell_line: bl21. Cellular_location: secreted. Gene: celz. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 23 models
Authors: E.Brun,F.Moriaud,P.Gans,M.J.Blackledge,F.Barras,D.Marion
Key ref:
E.Brun et al. (1997). Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi. Biochemistry, 36, 16074-16086. PubMed id: 9405041 DOI: 10.1021/bi9718494
Date:
30-Apr-97     Release date:   06-May-98    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07103  (GUNZ_DICD3) -  Endoglucanase Z from Dickeya dadantii (strain 3937)
Seq:
Struc: 		426 a.a.
62 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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/bi9718494 Biochemistry 36:16074-16086 (1997)
PubMed id: 9405041  
 
 
Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi.
E.Brun, F.Moriaud, P.Gans, M.J.Blackledge, F.Barras, D.Marion.
 
  ABSTRACT  
 
Two-dimensional proton nuclear magnetic resonance spectroscopy has been used to determine the three-dimensional structure of the 62 amino acid C-terminal cellulose-binding domain (CBD) of the endoglucanase Z (CBDEGZ), secreted by Erwinia chrysanthemi. An experimental data set comprising 958 interproton nOe-derived restraints was used to calculate 23 structures. The calculated structures have an average root-mean-square deviation between Cys4 and Cys61 of 0.91 +/- 0.11 A for backbone atoms and 1.18 +/- 0.12 A for the heavy atoms. The CBDEGZ exhibits a skiboot shape based mainly on a triple antiparallel beta-sheet perpendicular to a less-ordered summital loop. Three aromatic rings (Trp18, Trp43, and Tyr44) are localized on one face of the protein and are exposed to the solvent in a conformation compatible with a cellulose-binding site. Based on its original folding, we have been able to relate the CBD sequence to those of several domains of unknown function occurring in several bacterial chitinases as well as other proteins. This study also provides a structural basis for analyzing the secretion-related information specific to the CBDEGZ.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19458654 M.W.Delpin, and A.E.Goodman (2009).
Nutrient regime regulates complex transcriptional start site usage within a Pseudoalteromonas chitinase gene cluster.
  ISME J, 3, 1053-1063.  
17091272 K.Morimoto, M.Yoshimoto, S.Karita, T.Kimura, K.Ohmiya, and K.Sakka (2007).
Characterization of the third chitinase Chi18C of Clostridium paraputrificum M-21.
  Appl Microbiol Biotechnol, 73, 1106-1113.  
17294188 S.K.Park, C.W.Kim, H.Kim, J.S.Jung, and G.E.Harman (2007).
Cloning and high-level production of a chitinase from Chromobacterium sp. and the role of conserved or nonconserved residues on its catalytic activity.
  Appl Microbiol Biotechnol, 74, 791-804.  
16598448 Y.Itoh, J.Watanabe, H.Fukada, R.Mizuno, Y.Kezuka, T.Nonaka, and T.Watanabe (2006).
Importance of Trp59 and Trp60 in chitin-binding, hydrolytic, and antifungal activities of Streptomyces griseus chitinase C.
  Appl Microbiol Biotechnol, 72, 1176-1184.  
15784618 J.Flint, D.N.Bolam, D.Nurizzo, E.J.Taylor, M.P.Williamson, C.Walters, G.J.Davies, and H.J.Gilbert (2005).
Probing the mechanism of ligand recognition in family 29 carbohydrate-binding modules.
  J Biol Chem, 280, 23718-23726.
PDB codes: 1w8t 1w8u 1w8w 1w8z 1w90 1w9f 1wcu
15666145 W.J.Lim, S.Y.Hong, C.L.An, K.M.Cho, B.R.Choi, Y.K.Kim, J.M.An, J.M.Kang, S.M.Lee, S.J.Cho, H.Kim, and H.D.Yun (2005).
Construction of minimum size cellulase (Cel5Z) from Pectobacterium chrysanthemi PY35 by removal of the C-terminal region.
  Appl Microbiol Biotechnol, 68, 46-52.  
15604820 L.Hildén, and G.Johansson (2004).
Recent developments on cellulases and carbohydrate-binding modules with cellulose affinity.
  Biotechnol Lett, 26, 1683-1693.  
15019735 M.C.Chang, P.L.Lai, and M.L.Wu (2004).
Biochemical characterization and site-directed mutational analysis of the double chitin-binding domain from chitinase 92 of Aeromonas hydrophila JP101.
  FEMS Microbiol Lett, 232, 61-66.  
14635132 F.P.Wang, Q.Li, Y.Zhou, M.G.Li, and X.Xiao (2003).
The C-terminal module of Chi1 from Aeromonas caviae CB101 has a function in substrate binding and hydrolysis.
  Proteins, 53, 908-916.  
12562783 H.Orikoshi, N.Baba, S.Nakayama, H.Kashu, K.Miyamoto, M.Yasuda, Y.Inamori, and H.Tsujibo (2003).
Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. strain O-7.
  J Bacteriol, 185, 1153-1160.  
12571009 H.Tsujibo, T.Kubota, M.Yamamoto, K.Miyamoto, and Y.Inamori (2003).
Characterization of chitinase genes from an alkaliphilic actinomycete, Nocardiopsis prasina OPC-131.
  Appl Environ Microbiol, 69, 894-900.  
12788706 J.Gao, M.W.Bauer, K.R.Shockley, M.A.Pysz, and R.M.Kelly (2003).
Growth of hyperthermophilic archaeon Pyrococcus furiosus on chitin involves two family 18 chitinases.
  Appl Environ Microbiol, 69, 3119-3128.  
11872449 D.Y.Kobayashi, R.M.Reedy, J.Bick, and P.V.Oudemans (2002).
Characterization of a chitinase gene from Stenotrophomonas maltophilia strain 34S1 and its involvement in biological control.
  Appl Environ Microbiol, 68, 1047-1054.  
11772635 H.Tsujibo, H.Orikoshi, N.Baba, M.Miyahara, K.Miyamoto, M.Yasuda, and Y.Inamori (2002).
Identification and characterization of the gene cluster involved in chitin degradation in a marine bacterium, Alteromonas sp. strain O-7.
  Appl Environ Microbiol, 68, 263-270.  
11889092 K.Miyamoto, E.Nukui, H.Itoh, T.Sato, T.Kobayashi, C.Imada, E.Watanabe, Y.Inamori, and H.Tsujibo (2002).
Molecular analysis of the gene encoding a novel chitin-binding protease from Alteromonas sp. strain O-7 and its role in the chitinolytic system.
  J Bacteriol, 184, 1865-1872.  
12092819 Y.Itoh, T.Kawase, N.Nikaidou, H.Fukada, M.Mitsutomi, T.Watanabe, and Y.Itoh (2002).
Functional analysis of the chitin-binding domain of a family 19 chitinase from Streptomyces griseus HUT6037: substrate-binding affinity and cis-dominant increase of antifungal function.
  Biosci Biotechnol Biochem, 66, 1084-1092.  
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.  
11137603 A.Pourcher, L.Sutra, I.Hébé, G.Moguedet, C.Bollet, P.Simoneau, and L.Gardan (2001).
Enumeration and characterization of cellulolytic bacteria from refuse of a landfill.
  FEMS Microbiol Ecol, 34, 229-241.  
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
16233129 K.Morimoto, S.Karita, T.Kimura, K.Sakka, and K.Ohmiya (2001).
Characterization of Clostridium paraputrificum chitinase A from a recombinant Escherichia coli.
  J Biosci Bioeng, 92, 466-468.  
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.  
11160110 T.Lonhienne, K.Mavromatis, C.E.Vorgias, L.Buchon, C.Gerday, and V.Bouriotis (2001).
Cloning, sequences, and characterization of two chitinase genes from the Antarctic Arthrobacter sp. strain TAD20: isolation and partial characterization of the enzymes.
  J Bacteriol, 183, 1773-1779.  
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
10823940 D.M.van Aalten, B.Synstad, M.B.Brurberg, E.Hough, B.W.Riise, V.G.Eijsink, and R.K.Wierenga (2000).
Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
  Proc Natl Acad Sci U S A, 97, 5842-5847.
PDB code: 1e15
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
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.  
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.  
10760150 O.Francetic, C.Badaut, S.Rimsky, and A.P.Pugsley (2000).
The ChiA (YheB) protein of Escherichia coli K-12 is an endochitinase whose gene is negatively controlled by the nucleoid-structuring protein H-NS.
  Mol Microbiol, 35, 1506-1517.  
10978766 P.Tomme, A.Boraston, J.M.Kormos, R.A.Warren, and D.G.Kilburn (2000).
Affinity electrophoresis for the identification and characterization of soluble sugar binding by carbohydrate-binding modules.
  Enzyme Microb Technol, 27, 453-458.  
10819965 S.J.Charnock, D.N.Bolam, J.P.Turkenburg, H.J.Gilbert, L.M.Ferreira, G.J.Davies, and C.M.Fontes (2000).
The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain.
  Biochemistry, 39, 5013-5021.
PDB code: 1dyo
10788483 T.Ikegami, T.Okada, M.Hashimoto, S.Seino, T.Watanabe, and M.Shirakawa (2000).
Solution structure of the chitin-binding domain of Bacillus circulans WL-12 chitinase A1.
  J Biol Chem, 275, 13654-13661.
PDB code: 1ed7
  10419961 H.D.Simpson, and F.Barras (1999).
Functional analysis of the carbohydrate-binding domains of Erwinia chrysanthemi Cel5 (Endoglucanase Z) and an Escherichia coli putative chitinase.
  J Bacteriol, 181, 4611-4616.  
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.  
9818257 E.A.Bayer, H.Chanzy, R.Lamed, and Y.Shoham (1998).
Cellulose, cellulases and cellulosomes.
  Curr Opin Struct Biol, 8, 548-557.  
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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