PDBsum entry 1k42

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protein links
Hydrolase PDB id
Protein chain
168 a.a.
PDB id:
Name: Hydrolase
Title: The solution structure of the cbm4-2 carbohydrate binding module from a thermostable rhodothermus marinus xylanase.
Structure: Xylanase. Chain: a. Fragment: second family 4 carbohydrate binding module (cbm4-2)(residues 211-373). Engineered: yes
Source: Rhodothermus marinus. Organism_taxid: 29549. Gene: xyn10a. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 12 models
Authors: P.J.Simpson,S.J.Jamieson,M.Abou-Hachem,E.Nordberg-Karlsson, H.J.Gilbert,O.Holst,M.P.Williamson
Key ref:
P.J.Simpson et al. (2002). The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase. Biochemistry, 41, 5712-5719. PubMed id: 11980475 DOI: 10.1021/bi012093i
05-Oct-01     Release date:   29-May-02    
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Protein chain
Pfam   ArchSchema ?
P96988  (P96988_RHOMR) -  Xylanase (Fragment)
412 a.a.
168 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 149 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     hydrolase activity, acting on glycosyl bonds     1 term  


DOI no: 10.1021/bi012093i Biochemistry 41:5712-5719 (2002)
PubMed id: 11980475  
The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase.
P.J.Simpson, S.J.Jamieson, M.Abou-Hachem, E.N.Karlsson, H.J.Gilbert, O.Holst, M.P.Williamson.
The solution structure is presented for the second family 4 carbohydrate binding module (CBM4-2) of xylanase 10A from the thermophilic bacterium Rhodothermus marinus. CBM4-2, which binds xylan tightly, has a beta-sandwich structure formed by 11 strands, and contains a prominent cleft. From NMR titrations, it is shown that the cleft is the binding site for xylan, and that the main amino acids interacting with xylan are Asn31, Tyr69, Glu72, Phe110, Arg115, and His146. Key liganding residues are Tyr69 and Phe110, which form stacking interactions with the sugar. It is suggested that the loops on which the rings are displayed can alter their conformation on substrate binding, which may have functional importance. Comparison both with other family 4 cellulose binding modules and with the structurally similar family 22 xylan binding module shows that the key aromatic residues are in similar positions, and that the bottom of the cleft is much more hydrophobic in the cellulose binding modules than the xylan binding proteins. It is concluded that substrate specificity is determined by a combination of ring orientation and the nature of the residues lining the bottom of the binding cleft.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21219452 D.Dodd, R.I.Mackie, and I.K.Cann (2011).
Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes.
  Mol Microbiol, 79, 292-304.  
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
19878581 L.von Schantz, F.Gullfot, S.Scheer, L.Filonova, L.Cicortas Gunnarsson, J.E.Flint, G.Daniel, E.Nordberg-Karlsson, H.Brumer, and M.Ohlin (2009).
Affinity maturation generates greatly improved xyloglucan-specific carbohydrate binding modules.
  BMC Biotechnol, 9, 92.  
19682383 R.F.De Souza, L.M.Iyer, and L.Aravind (2009).
The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains.
  Biol Direct, 4, 25; discussion 25.  
18784084 M.E.Caines, H.Zhu, M.Vuckovic, L.M.Willis, S.G.Withers, W.W.Wakarchuk, and N.C.Strynadka (2008).
The Structural Basis for T-antigen Hydrolysis by Streptococcus pneumoniae: A TARGET FOR STRUCTURE-BASED VACCINE DESIGN.
  J Biol Chem, 283, 31279-31283.
PDB code: 3ecq
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.  
17935619 L.Filonova, L.C.Gunnarsson, G.Daniel, and M.Ohlin (2007).
Synthetic xylan-binding modules for mapping of pulp fibres and wood sections.
  BMC Plant Biol, 7, 54.  
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
16537424 L.McCartney, A.W.Blake, J.Flint, D.N.Bolam, A.B.Boraston, H.J.Gilbert, and J.P.Knox (2006).
Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules.
  Proc Natl Acad Sci U S A, 103, 4765-4770.  
16838297 R.Johansson, L.C.Gunnarsson, M.Ohlin, and S.Ohlson (2006).
Thermostable carbohydrate-binding modules in affinity chromatography.
  J Mol Recognit, 19, 275-281.  
16075163 S.H.Bjornsdottir, T.Blondal, G.O.Hreggvidsson, G.Eggertsson, S.Petursdottir, S.Hjorleifsdottir, S.H.Thorbjarnardottir, and J.K.Kristjansson (2006).
Rhodothermus marinus: physiology and molecular biology.
  Extremophiles, 10, 1.  
14738848 I.Levy, T.Paldi, and O.Shoseyov (2004).
Engineering a bifunctional starch-cellulose cross-bridge protein.
  Biomaterials, 25, 1841-1849.  
14990996 T.Mizushima, T.Hirao, Y.Yoshida, S.J.Lee, T.Chiba, K.Iwai, Y.Yamaguchi, K.Kato, T.Tsukihara, and K.Tanaka (2004).
Structural basis of sugar-recognizing ubiquitin ligase.
  Nat Struct Mol Biol, 11, 365-370.
PDB codes: 1umh 1umi
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.  
12831897 D.Shallom, and Y.Shoham (2003).
Microbial hemicellulases.
  Curr Opin Microbiol, 6, 219-228.  
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.