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PDBsum entry 1isx

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1isx
Jmol
Contents
Protein chains
436 a.a. *
Ligands
XYP-XYP-XYP ×3
XYP-XYP ×3
XYP ×2
Waters ×806
* Residue conservation analysis
PDB id:
1isx
Name: Hydrolase
Title: Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with xylotriose
Structure: Endo-1,4-beta-d-xylanase. Chain: a, b. Engineered: yes
Source: Streptomyces olivaceoviridis. Organism_taxid: 1921. Strain: e-86. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.189     R-free:   0.240
Authors: Z.Fujimoto,A.Kuno,S.Kaneko,H.Kobayashi,I.Kusakabe,H.Mizuno
Key ref:
Z.Fujimoto et al. (2002). Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module. J Mol Biol, 316, 65-78. PubMed id: 11829503 DOI: 10.1006/jmbi.2001.5338
Date:
27-Dec-01     Release date:   20-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7SI98  (Q7SI98_STROI) -  Hydrolase
Seq:
Struc:
436 a.a.
436 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.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1006/jmbi.2001.5338 J Mol Biol 316:65-78 (2002)
PubMed id: 11829503  
 
 
Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module.
Z.Fujimoto, A.Kuno, S.Kaneko, H.Kobayashi, I.Kusakabe, H.Mizuno.
 
  ABSTRACT  
 
The family 10 xylanase from Streptomyces olivaceoviridis E-86 contains a (beta/alpha)(8)-barrel as a catalytic domain, a family 13 carbohydrate binding module (CBM) as a xylan binding domain (XBD) and a Gly/Pro-rich linker between them. The crystal structure of this enzyme showed that XBD has three similar subdomains, as indicated by the presence of a triple-repeated sequence, forming a galactose binding lectin fold similar to that found in the ricin toxin B-chain. Comparison with the structure of ricin/lactose complex suggests three potential sugar binding sites in XBD. In order to understand how XBD binds to the xylan chain, we analyzed the sugar-complex structure by the soaking experiment method using the xylooligosaccharides and other sugars. In the catalytic cleft, bound sugars were observed in the xylobiose and xylotriose complex structures. In the XBD, bound sugars were identified in subdomains alpha and gamma in all of the complexes with xylose, xylobiose, xylotriose, glucose, galactose and lactose. XBD binds xylose or xylooligosaccharides at the same sugar binding sites as in the case of the ricin/lactose complex but its binding manner for xylose and xylooligosaccharides is different from the galactose binding mode in ricin, even though XBD binds galactose in the same manner as in the ricin/galactose complex. These different binding modes are utilized efficiently and differently to bind the long substrate to xylanase and ricin-type lectin. XBD can bind any xylose in the xylan backbone, whereas ricin-type lectin recognizes the terminal galactose to sandwich the large sugar chain, even though the two domains have the same family 13 CBM structure. Family 13 CBM has rather loose and broad sugar specificities and is used by some kinds of proteins to bind their target sugars. In such enzyme, XBD binds xylan, and the catalytic domain may assume a flexible position with respect to the XBD/xylan complex, inasmuch as the linker region is unstructured.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo view of the ribbon model of FXYN/X2 complex. The catalytic domain, linker, and subdomains a, b, g of XBD are drawn in green, black, blue, yellow and pink, respectively. Two catalytic residues are displayed in red. Soaked xylose units and disulfide bonds are indicated by ball-and-stick drawings. The figure was drawn with the program Raster3d.[46 and 47]
Figure 5.
Figure 5. Stereo views of the sugar binding structures in the XBD with the F[obs] - F[calc] omit electron density maps contoured at 3s. (a) In the subdomain a in the FXYN/X2 complex, (b) subdomain g in the FXYN/X3 complex, (c) subdomain g in the FXYN/Glc complex, (d) subdomain a in the FXYN/Gal complex, (e) subdomain g in the FXYN/Lac complex, and (f) subdomain a in the FXYN/Lac complex from a different view point. Hydrogen bonding interactions between the enzyme and sugars are indicated by broken lines. Carbon numbers of bound xylose are indicated.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 65-78) copyright 2002.  
  Figures were selected by the author.  

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
20842142 A.Takahashi, J.Inokoshi, M.Tsunoda, K.Suzuki, A.Takenaka, T.Sekiguchi, S.Omura, and H.Tanaka (2010).
Actinohivin: specific amino acid residues essential for anti-HIV activity.
  J Antibiot (Tokyo), 63, 661-665.  
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.  
19608743 H.Ichinose, Z.Fujimoto, M.Honda, K.Harazono, Y.Nishimoto, A.Uzura, and S.Kaneko (2009).
A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27.
  J Biol Chem, 284, 25097-25106.
PDB codes: 3a21 3a22 3a23
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
19107475 N.Li, P.Shi, P.Yang, Y.Wang, H.Luo, Y.Bai, Z.Zhou, and B.Yao (2009).
A xylanase with high pH stability from Streptomyces sp. S27 and its carbohydrate-binding module with/without linker-region-truncated versions.
  Appl Microbiol Biotechnol, 83, 99.  
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
17121820 D.K.Poon, S.G.Withers, and L.P.McIntosh (2007).
Direct demonstration of the flexibility of the glycosylated proline-threonine linker in the Cellulomonas fimi Xylanase Cex through NMR spectroscopic analysis.
  J Biol Chem, 282, 2091-2100.  
16672498 H.Ichinose, A.Kuno, T.Kotake, M.Yoshida, K.Sakka, J.Hirabayashi, Y.Tsumuraya, and S.Kaneko (2006).
Characterization of an exo-beta-1,3-galactanase from Clostridium thermocellum.
  Appl Environ Microbiol, 72, 3515-3523.  
16247799 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, and N.Tanaka (2005).
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
  Proteins, 61, 999.
PDB codes: 1vbr 1vbu
15914908 M.Nishimoto, M.Kitaoka, S.Fushinobu, and K.Hayashi (2005).
The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases.
  Biosci Biotechnol Biochem, 69, 904-910.  
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.  
14747719 M.Nishimoto, S.Fushinobu, A.Miyanaga, T.Wakagi, H.Shoun, K.Sakka, K.Ohmiya, S.Nirasawa, M.Kitaoka, and K.Hayashi (2004).
Crystallization and preliminary X-ray analysis of xylanase B from Clostridium stercorarium.
  Acta Crystallogr D Biol Crystallogr, 60, 342-343.  
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.  
15162495 R.Koike, K.Kinoshita, and A.Kidera (2004).
Probabilistic description of protein alignments for sequences and structures.
  Proteins, 56, 157-166.  
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.  
15078885 S.Kaneko, H.Ichinose, Z.Fujimoto, A.Kuno, K.Yura, M.Go, H.Mizuno, I.Kusakabe, and H.Kobayashi (2004).
Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex.
  J Biol Chem, 279, 26619-26626.
PDB code: 1v6y
15194688 T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, and T.Hatakeyama (2004).
Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism.
  J Biol Chem, 279, 37133-37141.
PDB code: 1vcl
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.  
12364335 M.Tenno, A.Saeki, F.J.Kézdy, A.P.Elhammer, and A.Kurosaka (2002).
The lectin domain of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1 is involved in O-glycosylation of a polypeptide with multiple acceptor sites.
  J Biol Chem, 277, 47088-47096.  
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.