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PDBsum entry 1i8a

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protein ligands metals links
Hydrolase PDB id
1i8a
Jmol
Contents
Protein chain
189 a.a. *
Ligands
BGC
Metals
_CA ×3
Waters ×163
* Residue conservation analysis
PDB id:
1i8a
Name: Hydrolase
Title: Family 9 carbohydrate-binding module from thermotoga maritima xylanase 10a with glucose
Structure: Endo-1,4-beta-xylanase a. Chain: a. Fragment: c2 domain (residues 871-1059). Synonym: xylanase a. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.90Å     R-factor:   0.201     R-free:   0.217
Authors: V.Notenboom,A.B.Boraston,R.A.J.Warren,D.G.Kilburn,D.R.Rose
Key ref:
V.Notenboom et al. (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. PubMed id: 11371186 DOI: 10.1021/bi0101704
Date:
12-Mar-01     Release date:   13-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q60037  (XYNA_THEMA) -  Endo-1,4-beta-xylanase A
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1059 a.a.
189 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.8  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate catabolic process   1 term 
  Biochemical function     carbohydrate binding     2 terms  

 

 
DOI no: 10.1021/bi0101704 Biochemistry 40:6248-6256 (2001)
PubMed id: 11371186  
 
 
Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms.
V.Notenboom, A.B.Boraston, D.G.Kilburn, D.R.Rose.
 
  ABSTRACT  
 
The C-terminal module of the thermostable Thermotoga maritima xylanase 10A (CBM9-2) is a family 9 carbohydrate-binding module that binds to amorphous and crystalline cellulose and a range of soluble di- and monosaccharides as well as to cello and xylo oligomers of different degrees of polymerization [Boraston, A. B., Creagh, A. L., Alam, Md. M., Kormos, J. M., Tomme, P., Haynes, C. A., Warren, R. A. J., and Kilburn, D. G. (2001) Biochemistry 40, 6240-6247]. The crystal structure of CBM9-2 has been determined by the multiwavelength anomalous dispersion method to 1.9 A resolution. CBM9-2 assumes a beta-sandwich fold and contains three metal binding sites. The bound metal atoms, which are most likely calcium cations, are in an octahedral coordination. The crystal structures of CBM9-2 in complex with glucose and cellobiose were also determined in order to identify the sugar-binding site and provide insight into the structural basis for sugar binding by CBM9-2. The sugar-binding site is a solvent-exposed slot sufficient in depth, width, and length to accommodate a disaccharide. Two tryptophan residues are stacked together on the surface of the protein forming the sugar-binding site. From the complex structures with glucose and cellobiose, it was inferred that CBM9-2 binds exclusively to the reducing end of mono-, di-, and oligosaccharides with an intricate hydrogen-bonding network involving mainly charged residues, as well as stacking interactions by Trp175 and Trp71. The binding interactions are limited to disaccharides as was expected from calorimetric data. Comparison of the glucose and cellobiose complexes revealed surprising differences in binding of these two substrates by CBM9-2. Cellobiose was found to bind in a distinct orientation from glucose, while still maintaining optimal stacking and electrostatic interactions with the reducing end sugar.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20593184 Y.L.Jiao, S.J.Wang, M.S.Lv, J.L.Xu, Y.W.Fang, and S.Liu (2011).
A GH57 family amylopullulanase from deep-sea Thermococcus siculi: expression of the gene and characterization of the recombinant enzyme.
  Curr Microbiol, 62, 222-228.  
  20944224 A.P.Yeh, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, X.Cai, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1287-1296.
PDB code: 3hbz
19908036 D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.
  Appl Microbiol Biotechnol, 85, 1241-1249.  
19496182 M.Kavoosi, A.L.Creagh, R.F.Turner, D.G.Kilburn, and C.A.Haynes (2009).
Direct measurement of the kinetics of CBM9 fusion-tag bioprocessing using luminescence resonance energy transfer.
  Biotechnol Prog, 25, 874-881.  
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
18083821 W.Liebl, C.Winterhalter, W.Baumeister, M.Armbrecht, and M.Valdez (2008).
Xylanase attachment to the cell wall of the hyperthermophilic bacterium Thermotoga maritima.
  J Bacteriol, 190, 1350-1358.  
17006740 G.Mamo, R.Hatti-Kaul, and B.Mattiasson (2007).
Fusion of carbohydrate binding modules from Thermotoga neapolitana with a family 10 xylanase from Bacillus halodurans S7.
  Extremophiles, 11, 169-177.  
18032609 L.Cuthbertson, M.S.Kimber, and C.Whitfield (2007).
Substrate binding by a bacterial ABC transporter involved in polysaccharide export.
  Proc Natl Acad Sci U S A, 104, 19529-19534.
PDB code: 2r5o
17878204 L.M.Iyer, V.Anantharaman, and L.Aravind (2007).
The DOMON domains are involved in heme and sugar recognition.
  Bioinformatics, 23, 2660-2664.  
17394253 M.Kavoosi, A.L.Creagh, D.G.Kilburn, and C.A.Haynes (2007).
Strategy for selecting and characterizing linker peptides for CBM9-tagged fusion proteins expressed in Escherichia coli.
  Biotechnol Bioeng, 98, 599-610.  
16962969 D.P.Kloer, C.Hagel, J.Heider, and G.E.Schulz (2006).
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.
  Structure, 14, 1377-1388.
PDB code: 2ivf
16461704 F.J.Stjohn, J.D.Rice, and J.F.Preston (2006).
Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization.
  Appl Environ Microbiol, 72, 1496-1506.  
16513741 H.S.Lee, K.R.Shockley, G.J.Schut, S.B.Conners, C.I.Montero, M.R.Johnson, C.J.Chou, S.L.Bridger, N.Wigner, S.D.Brehm, F.E.Jenney, D.A.Comfort, R.M.Kelly, and M.W.Adams (2006).
Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus.
  J Bacteriol, 188, 2115-2125.  
16601125 J.Henshaw, A.Horne-Bitschy, A.L.van Bueren, V.A.Money, D.N.Bolam, M.Czjzek, N.A.Ekborg, R.M.Weiner, S.W.Hutcheson, G.J.Davies, A.B.Boraston, and H.J.Gilbert (2006).
Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.
  J Biol Chem, 281, 17099-17107.
PDB codes: 2cdo 2cdp
16550304 J.Kleine, and W.Liebl (2006).
Comparative characterization of deletion derivatives of the modular xylanase XynA of Thermotoga maritima.
  Extremophiles, 10, 373-381.  
15501830 A.L.van Bueren, C.Morland, H.J.Gilbert, and A.B.Boraston (2005).
Family 6 carbohydrate binding modules recognize the non-reducing end of beta-1,3-linked glucans by presenting a unique ligand binding surface.
  J Biol Chem, 280, 530-537.
PDB codes: 1w9s 1w9t 1w9w
15643631 H.Lam, M.Kavoosi, C.A.Haynes, D.I.Wang, and D.Blankschtein (2005).
Affinity-enhanced protein partitioning in decyl beta-D-glucopyranoside two-phase aqueous micellar systems.
  Biotechnol Bioeng, 89, 381-392.  
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
16080150 P.Herman, J.Vecer, I.Barvik, V.Scognamiglio, M.Staiano, M.de Champdoré, A.Varriale, M.Rossi, and S.D'Auria (2005).
The role of calcium in the conformational dynamics and thermal stability of the D-galactose/D-glucose-binding protein from Escherichia coli.
  Proteins, 61, 184-195.  
15004012 D.N.Bolam, H.Xie, G.Pell, D.Hogg, G.Galbraith, B.Henrissat, and H.J.Gilbert (2004).
X4 modules represent a new family of carbohydrate-binding modules that display novel properties.
  J Biol Chem, 279, 22953-22963.  
14738848 I.Levy, T.Paldi, and O.Shoseyov (2004).
Engineering a bifunctional starch-cellulose cross-bridge protein.
  Biomaterials, 25, 1841-1849.  
14660574 M.Mizuno, T.Tonozuka, S.Suzuki, R.Uotsu-Tomita, S.Kamitori, A.Nishikawa, and Y.Sakano (2004).
Structural insights into substrate specificity and function of glucodextranase.
  J Biol Chem, 279, 10575-10583.
PDB codes: 1ug9 1ulv
15242594 S.Jamal-Talabani, A.B.Boraston, J.P.Turkenburg, N.Tarbouriech, V.M.Ducros, and G.J.Davies (2004).
Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules.
  Structure, 12, 1177-1187.
PDB codes: 1ux7 1w0n
12964193 A.Laederach, and P.J.Reilly (2003).
Specific empirical free energy function for automated docking of carbohydrates to proteins.
  J Comput Chem, 24, 1748-1757.  
12493836 E.García-Hernández, R.A.Zubillaga, E.A.Chavelas-Adame, E.Vázquez-Contreras, A.Rojo-Domínguez, and M.Costas (2003).
Structural energetics of protein-carbohydrate interactions: Insights derived from the study of lysozyme binding to its natural saccharide inhibitors.
  Protein Sci, 12, 135-142.  
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.  
14660338 Y.Ito, T.Tomita, N.Roy, A.Nakano, N.Sugawara-Tomita, S.Watanabe, N.Okai, N.Abe, and Y.Kamio (2003).
Cloning, expression, and cell surface localization of Paenibacillus sp. strain W-61 xylanase 5, a multidomain xylanase.
  Appl Environ Microbiol, 69, 6969-6978.  
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.  
11980476 M.Abou-Hachem, E.N.Karlsson, P.J.Simpson, S.Linse, P.Sellers, M.P.Williamson, S.J.Jamieson, H.J.Gilbert, D.N.Bolam, and O.Holst (2002).
Calcium binding and thermostability of carbohydrate binding module CBM4-2 of Xyn10A from Rhodothermus marinus.
  Biochemistry, 41, 5720-5729.  
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
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
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.