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PDBsum entry 1i1x

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protein links
Hydrolase PDB id
1i1x
Jmol
Contents
Protein chain
302 a.a. *
Waters ×267
* Residue conservation analysis
PDB id:
1i1x
Name: Hydrolase
Title: 1.11 a atomic resolution structure of a thermostable xylanase from thermoascus aurantiacus
Structure: Endo-1,4-beta-xylanase. Chain: a. Synonym: xylanase, 1,4-beta-d-xylan xylanohydrolase. Ec: 3.2.1.8
Source: Thermoascus aurantiacus. Organism_taxid: 5087. Strain: strain isolated from local indian soil
Resolution:
1.11Å     R-factor:   0.099     R-free:   0.124
Authors: R.Natesh,S.Ramakumar,M.A.Viswamitra
Key ref:
R.Natesh et al. (2003). Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy. Acta Crystallogr D Biol Crystallogr, 59, 105-117. PubMed id: 12499546
Date:
04-Feb-01     Release date:   07-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23360  (XYNA_THEAU) -  Endo-1,4-beta-xylanase
Seq:
Struc:
329 a.a.
302 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 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   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
Acta Crystallogr D Biol Crystallogr 59:105-117 (2003)
PubMed id: 12499546  
 
 
Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy.
R.Natesh, K.Manikandan, P.Bhanumoorthy, M.A.Viswamitra, S.Ramakumar.
 
  ABSTRACT  
 
Thermoascus aurantiacus xylanase is a thermostable enzyme which hydrolyses xylan, a major hemicellulose component of the biosphere. The crystal structure of this F/10 family xylanase, which has a triosephosphate isomerase (TIM) barrel (beta/alpha)(8) fold, has been solved to small-molecule accuracy at atomic resolution (1.11 A) at 293 K (RTUX) and at ultrahigh resolution (0.89 A) at 100 K (CTUX) using X-ray diffraction data sets collected on a synchrotron light source, resulting in R/R(free) values of 9.94/12.36 and 9.00/10.61% (for all data), respectively. Both structures were refined with anisotropic atomic displacement parameters. The 0.89 A structure, with 177 476 observed unique reflections, was refined without any stereochemical restraints during the final stages. The salt bridge between Arg124 and Glu232, which is bidentate in RTUX, is water-mediated in CTUX, suggesting the possibility of plasticity of ion pairs in proteins, with water molecules mediating some of the alternate arrangements. Two buried waters present inside the barrel form hydrogen-bond interactions with residues in strands beta2, beta3, beta4 and beta7 and presumably contribute to structural stability. The availability of accurate structural information at two different temperatures enabled the study of the temperature-dependent deformations of the TIM-barrel fold of the xylanase. Analysis of the deviation of corresponding C(alpha) atoms between RTUX and CTUX suggests that the interior beta-strands are less susceptible to changes as a function of temperature than are the alpha-helices, which are on the outside of the barrel. betaalpha-loops, which are longer and contribute residues to the active-site region, are more flexible than alphabeta-loops. The 0.89 A structure represents one of the highest resolution structures of a protein of such size with one monomer molecule in the asymmetric unit and also represents the highest resolution TIM-barrel fold structure to date. It may provide a useful template for theoretical modelling studies of the structure and dynamics of the ubiquitous TIM-barrel fold.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16823036 K.Manikandan, A.Bhardwaj, N.Gupta, N.K.Lokanath, A.Ghosh, V.S.Reddy, and S.Ramakumar (2006).
Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.
  Protein Sci, 15, 1951-1960.
PDB codes: 2f8q 2fgl
  16511146 K.Manikandan, A.Bhardwaj, A.Ghosh, V.S.Reddy, and S.Ramakumar (2005).
Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 747-749.  
15281129 K.Manikandan, and S.Ramakumar (2004).
The occurrence of C--H...O hydrogen bonds in alpha-helices and helix termini in globular proteins.
  Proteins, 56, 768-781.  
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.