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PDBsum entry 1knm
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Hydrolase PDB id
1knm

 

 

 

 

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Contents
Protein chain
129 a.a. *
Ligands
BGC-GAL ×2
GOL
Waters ×237
* Residue conservation analysis
PDB id:
1knm
Name: Hydrolase
Title: Streptomyces lividans xylan binding domain cbm13 in complex with lactose
Structure: Endo-1,4-beta-xylanase a. Chain: a. Fragment: carbohydrate binding module (residues 348-477). Synonym: xylanase a, 1,4-beta-d-xylan xylanohydrolase a. Engineered: yes
Source: Streptomyces lividans. Organism_taxid: 1916. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.20Å     R-factor:   0.126     R-free:   0.169
Authors: V.Notenboom,A.B.Boraston,S.J.Williams,D.G.Kilburn,D.R.Rose
Key ref:
V.Notenboom et al. (2002). High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding. Biochemistry, 41, 4246-4254. PubMed id: 11914070 DOI: 10.1021/bi015865j
Date:
19-Dec-01     Release date:   19-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26514  (XYNA_STRLI) -  Endo-1,4-beta-xylanase A from Streptomyces lividans
Seq:
Struc: 		477 a.a.
129 a.a.
Key:    PfamA 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.

 

 
DOI no: 10.1021/bi015865j Biochemistry 41:4246-4254 (2002)
PubMed id: 11914070  
 
 
High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding.
V.Notenboom, A.B.Boraston, S.J.Williams, D.G.Kilburn, D.R.Rose.
 
  ABSTRACT  
 
Carbohydrate-binding module (CBM) family 13 includes the "R-type" or "ricin superfamily" beta-trefoil lectins. The C-terminal CBM, CBM13, of xylanase 10A from Streptomyces lividans is a family 13 CBM that is not only structurally similar to the "R-type" lectins but also somewhat functionally similar. The primary function of CBM13 is to bind the polysaccharide xylan, but it retains the ability of the R-type lectins to bind small sugars such as lactose and galactose. The association of CBM13 with xylan appears to involve cooperative and additive participation of three binding pockets in each of the three trefoil domains of CBM13, suggesting a novel mechanism of CBM-xylan interaction. Thus, the interaction of CBM13 with sugars displays considerable plasticity for which we provide a structural rationale. The high-resolution crystal structure of CBM13 was determined by multiple anomalous dispersion from a complex of CBM13 with a brominated ligand. Crystal structures of CBM13 in complex with lactose and xylopentaose revealed two distinct mechanisms of ligand binding. CBM13 has retained its specificity for lactose via Ricin-like binding in all of the three classic trefoil binding pockets. However, CBM13 has the ability to bind either the nonreducing galactosyl moiety or the reducing glucosyl moiety of lactose. The mode of xylopentaose binding suggests adaptive mutations in the trefoil sugar binding scaffold to accommodate internal binding on helical polymers of xylose.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21514389 J.P.Yang, X.X.Ma, Y.X.He, W.F.Li, Y.Kang, R.Bao, Y.Chen, and C.Z.Zhou (2011).
Crystal structure of the 30K protein from the silkworm Bombyx mori reveals a new member of the β-trefoil superfamily.
  J Struct Biol, 175, 97.
PDB code: 3pub
19292877 H.Hemmi, A.Kuno, S.Ito, R.Suzuki, T.Hasegawa, and J.Hirabayashi (2009).
NMR studies on the interaction of sugars with the C-terminal domain of an R-type lectin from the earthworm Lumbricus terrestris.
  FEBS J, 276, 2095-2105.  
18798567 L.Maveyraud, H.Niwa, V.Guillet, D.I.Svergun, P.V.Konarev, R.A.Palmer, W.J.Peumans, P.Rougé, E.J.Van Damme, C.D.Reynolds, and L.Mourey (2009).
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.
  Proteins, 75, 89.
PDB codes: 3c9z 3ca0 3ca1 3ca3 3ca4 3ca5 3ca6 3cah
18384043 G.André-Leroux, J.G.Berrin, J.Georis, F.Arnaut, and N.Juge (2008).
Structure-based mutagenesis of Penicillium griseofulvum xylanase using computational design.
  Proteins, 72, 1298-1307.  
16550304 J.Kleine, and W.Liebl (2006).
Comparative characterization of deletion derivatives of the modular xylanase XynA of Thermotoga maritima.
  Extremophiles, 10, 373-381.  
16707677 L.E.Taylor, B.Henrissat, P.M.Coutinho, N.A.Ekborg, S.W.Hutcheson, and R.M.Weiner (2006).
Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T.
  J Bacteriol, 188, 3849-3861.  
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
16607570 V.Spiwok, P.Lipovová, T.Skálová, E.Vondrácková, J.Dohnálek, J.Hasek, and B.Králová (2005).
Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance.
  J Comput Aided Mol Des, 19, 887-901.  
15292273 A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
  J Biol Chem, 279, 44907-44914.
PDB codes: 1wd3 1wd4
15004011 J.L.Henshaw, D.N.Bolam, V.M.Pires, M.Czjzek, B.Henrissat, L.M.Ferreira, C.M.Fontes, and H.J.Gilbert (2004).
The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities.
  J Biol Chem, 279, 21552-21559.  
14997539 M.S.Sujatha, and P.V.Balaji (2004).
Identification of common structural features of binding sites in galactose-specific proteins.
  Proteins, 55, 44-65.  
15388944 R.Suzuki, Z.Fujimoto, A.Kuno, J.Hirabayashi, K.Kasai, and T.Hasegawa (2004).
Crystallization and preliminary X-ray crystallographic studies of the C-terminal domain of galactose-binding lectin EW29 from the earthworm Lumbricus terrestris.
  Acta Crystallogr D Biol Crystallogr, 60, 1895-1896.  
15184164 Y.Brennan, W.N.Callen, L.Christoffersen, P.Dupree, F.Goubet, S.Healey, M.Hernández, M.Keller, K.Li, N.Palackal, A.Sittenfeld, G.Tamayo, S.Wells, G.P.Hazlewood, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
Unusual microbial xylanases from insect guts.
  Appl Environ Microbiol, 70, 3609-3617.  
14670957 Z.Fujimoto, S.Kaneko, A.Kuno, H.Kobayashi, I.Kusakabe, and H.Mizuno (2004).
Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86.
  J Biol Chem, 279, 9606-9614.
PDB codes: 1v6u 1v6v 1v6w 1v6x
12831897 D.Shallom, and Y.Shoham (2003).
Microbial hemicellulases.
  Curr Opin Microbiol, 6, 219-228.  
12538902 R.Olson, and E.Gouaux (2003).
Vibrio cholerae cytolysin is composed of an alpha-hemolysin-like core.
  Protein Sci, 12, 379-383.  
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.

 

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