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PDBsum entry 1gok

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protein links
Hydrolase PDB id
1gok
Jmol
Contents
Protein chain
303 a.a. *
Waters ×248
* Residue conservation analysis
PDB id:
1gok
Name: Hydrolase
Title: Thermostable xylanase i from thermoascus aurantiacus- crystal form ii
Structure: Endo-1,4-beta-xylanase. Chain: a. Synonym: xylanase, 1,4-beta-d-xylan xylanohydrolase, taxi. Ec: 3.2.1.8
Source: Thermoascus aurantiacus. Organism_taxid: 5087
Resolution:
1.14Å     R-factor:   0.180     R-free:   0.193
Authors: L.Lo Leggio,R.W.Pickersgill
Key ref:
L.Lo Leggio et al. (2001). Substrate specificity and subsite mobility in T. aurantiacus xylanase 10A. FEBS Lett, 509, 303-308. PubMed id: 11741607 DOI: 10.1016/S0014-5793(01)03177-5
Date:
22-Oct-01     Release date:   25-Oct-01    
Supersedes: 1tax
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 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  

 

 
DOI no: 10.1016/S0014-5793(01)03177-5 FEBS Lett 509:303-308 (2001)
PubMed id: 11741607  
 
 
Substrate specificity and subsite mobility in T. aurantiacus xylanase 10A.
L.Lo Leggio, S.Kalogiannis, K.Eckert, S.C.Teixeira, M.K.Bhat, C.Andrei, R.W.Pickersgill, S.Larsen.
 
  ABSTRACT  
 
The substrate specificity of Thermoascus aurantiacus xylanase 10A (TAX) has been investigated both biochemically and structurally. High resolution crystallographic analyses at 291 K and 100 K of TAX complexes with xylobiose show that the ligand is in its alpha anomeric conformation and provide a rationale for specificity on p-nitrophenyl glycosides at the -1 and -2 subsites. Trp 275, which is disordered in uncomplexed structures, is stabilised by its interaction with xylobiose. Two structural subsets in family 10 are identified, which differ by the presence or absence of a short helical stretch in the eighth betaalpha-loop of the TIM barrel, the loop bearing Trp 275. This structural difference is discussed in the context of Trp 275 mobility and xylanase function.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Xylobiose and glycerol binding in TAX. TAX residues are shown for the XBCRYO structure in red, magenta (tryptophan residues forming the aromatic cage at subsite −1) or orange (catalytic glutamates). Xylobiose and water 75 in the XBCRYO structure is shown in blue. The sugar moieties occupying subsites −2, −1 and +1 in XBRT and water 319 are shown in cyan. Glycerol and water 203 from the GLC structure are shown in green. Potential hydrogen bonds with TAX (distances shorter than 3.2 Å) are coloured according to the same scheme as for the ligands. The substrate binding groove is oriented so that subsite −2 is at the top and subsite +1 is at the bottom. In panel b a Sigmaa F[obs]−F[calc] map calculated prior to incorporation of xylobiose in the model (blue) is shown for XBCRYO contoured at 2σ around 1.5 Å from xylobiose. In white the conformation of xylobiose bound to the P. simplicissimum xylanase (PDB code 1B3W), is shown for comparison. In panel c a simulated annealing 2F[obs]−F[calc] omit map is shown for the xylose at subsite +1 in the XBRT model (cyan) contoured at 0.7σ. The complexes of P. simplicissimum xylanase with xylotetraose (PDB code 1B3Y) and xylopentaose (PDB code 1B3Z) are shown in white, and the complex of P. fluorescens xylanase 10A with xylopentaose (PDB code 1E5N) is shown in purple for comparison.
Figure 2.
Fig. 2. Alternative conformations for Glu 46, Trp 275 and Arg 276 in the form II crystal.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2001, 509, 303-308) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15981268 E.Ben-Zeev, N.Kowalsman, A.Ben-Shimon, D.Segal, T.Atarot, O.Noivirt, T.Shay, and M.Eisenstein (2005).
Docking to single-domain and multiple-domain proteins: old and new challenges.
  Proteins, 60, 195-201.  
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
15765251 M.K.Ali, F.B.Rudolph, and G.N.Bennett (2005).
Characterization of thermostable Xyn10A enzyme from mesophilic Clostridium acetobutylicum ATCC 824.
  J Ind Microbiol Biotechnol, 32, 12-18.  
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.  
15522513 M.Díaz, S.Rodriguez, J.M.Fernández-Abalos, J.De Las Rivas, A.Ruiz-Arribas, V.L.Shnyrov, and R.I.Santamaría (2004).
Single mutations of residues outside the active center of the xylanase Xys1 Delta from Streptomyces halstedii JM8 affect its activity.
  FEMS Microbiol Lett, 240, 237-243.  
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.  
12876348 A.Canals, M.C.Vega, F.X.Gomis-Rüth, M.Díaz, R.I.Santamaría R, and M.Coll (2003).
Structure of xylanase Xys1delta from Streptomyces halstedii.
  Acta Crystallogr D Biol Crystallogr, 59, 1447-1453.
PDB code: 1nq6
  16233324 M.Nishimoto, M.Kitaoka, and K.Hayashi (2002).
Employing chimeric xylanases to identify regions of an alkaline xylanase participating in enzyme activity at basic pH.
  J Biosci Bioeng, 94, 395-400.  
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.