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Serine hydrolase PDB id
1bs9
Jmol
Contents
Protein chain
207 a.a. *
Ligands
SO4
Waters ×143
* Residue conservation analysis
PDB id:
1bs9
Name: Serine hydrolase
Title: Acetylxylan esterase from p. Purpurogenum refined at 1.10 angstroms
Structure: Acetyl xylan esterase. Chain: a. Ec: 3.1.1.6
Source: Penicillium purpurogenum. Organism_taxid: 28575
Resolution:
1.10Å     R-factor:   0.123     R-free:   0.182
Authors: D.Ghosh,M.Erman,M.W.Sawicki,P.Lala,D.R.Weeks,N.Li, W.Pangborn,D.J.Thiel,H.Jornvall,J.Eyzaguirre
Key ref:
D.Ghosh et al. (1999). Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase. Acta Crystallogr D Biol Crystallogr, 55, 779-784. PubMed id: 10089308 DOI: 10.1107/S0907444999000244
Date:
01-Sep-98     Release date:   18-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O59893  (AXE2_PENPU) -  Acetylxylan esterase 2
Seq:
Struc: 		234 a.a.
207 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.72  - Acetylxylan esterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deacetylation of xylans and xylo-oligosaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1107/S0907444999000244 Acta Crystallogr D Biol Crystallogr 55:779-784 (1999)
PubMed id: 10089308  
 
 
Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase.
D.Ghosh, M.Erman, M.Sawicki, P.Lala, D.R.Weeks, N.Li, W.Pangborn, D.J.Thiel, H.Jörnvall, R.Gutierrez, J.Eyzaguirre.
 
  ABSTRACT  
 
Enzymatic and non-enzymatic iodination of the amino acid tyrosine is a well known phenomenon. The iodination technique has been widely used for labeling proteins. Using high-resolution X-ray crystallographic techniques, the chemical and three-dimensional structures of iodotyrosines formed by non-enzymatic incorporation of I atoms into tyrosine residues of a crystalline protein are described. Acetylxylan esterase (AXE II; 207 amino-acid residues) from Penicillium purpurogenum has substrate specificities towards acetate esters of D-xylopyranose residues in xylan and belongs to a new class of alpha/beta hydrolases. The crystals of the enzyme are highly ordered, tightly packed and diffract to better than sub-angström resolution at 85 K. The iodination technique has been utilized to prepare an isomorphous derivative of the AXE II crystal. The structure of the enzyme determined at 1.10 A resolution exclusively by normal and anomalous scattering from I atoms, along with the structure of the iodinated complex at 1.80 A resolution, demonstrate the formation of covalent bonds between I atoms and C atoms at ortho positions to the hydroxyl groups of two tyrosyl moieties, yielding iodotyrosines.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 2F[o] - F[c] electron-density maps for the native (blue; 1.10 Å resolution, contoured at 1.2 ) and iodinated complex (magenta; 1.80 Å resolution, contoured at 1.2 ) with their corresponding refined models (green, native; yellow, iodinated derivative) for (a) Tyr33 and (b) Tyr177. I atoms were not included in the phase calculation. 		Figure 4.
Figure 4 The mechanism of the iodination reaction could involve a normal aromatic electrophilic substitution by iodonium ion.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 779-784) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
19897648 S.Yoshida, R.I.Mackie, and I.K.Cann (2010).
Biochemical and domain analyses of FSUAxe6B, a modular acetyl xylan esterase, identify a unique carbohydrate binding module in Fibrobacter succinogenes S85.
  J Bacteriol, 192, 483-493.  
19185510 Z.Liu, and R.R.Julian (2009).
Deciphering the peptide iodination code: influence on subsequent gas-phase radical generation with photodissociation ESI-MS.
  J Am Soc Mass Spectrom, 20, 965-971.  
18060506 M.Colombres, J.A.Garate, C.F.Lagos, R.Araya-Secchi, P.Norambuena, S.Quiroz, L.Larrondo, T.Pérez-Acle, and J.Eyzaguirre (2008).
An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum.
  J Comput Aided Mol Des, 22, 19-28.  
17428344 N.C.Rockwell, and J.C.Lagarias (2007).
Flexible mapping of homology onto structure with homolmapper.
  BMC Bioinformatics, 8, 123.  
17239398 P.Liu, H.E.Ewis, P.C.Tai, C.D.Lu, and I.T.Weber (2007).
Crystal structure of the Geobacillus stearothermophilus carboxylesterase Est55 and its activation of prodrug CPT-11.
  J Mol Biol, 367, 212-223.
PDB codes: 2ogs 2ogt
10944388 V.Z.Pletnev, T.S.Zamolodchikova, W.A.Pangborn, and W.L.Duax (2000).
Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities.
  Proteins, 41, 8.
PDB code: 1euf
10607665 M.Nardini, and B.W.Dijkstra (1999).
Alpha/beta hydrolase fold enzymes: the family keeps growing.
  Curr Opin Struct Biol, 9, 732-737.  
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.