PDBsum entry 2uve

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Hydrolase PDB id
Jmol PyMol
Protein chains
571 a.a. *
SO4 ×19
_NI ×9
Waters ×463
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of yersinia enterocolitica family 28 exopolygalacturonase
Structure: Exopolygalacturonase. Chain: a, b. Synonym: yegh28. Engineered: yes
Source: Yersinia enterocolitica. Organism_taxid: 630. Atcc: 9610. Expressed in: escherichia coli. Expression_system_taxid: 562
2.19Å     R-factor:   0.187     R-free:   0.228
Authors: D.W.Abbott,A.B.Boraston
Key ref:
D.W.Abbott and A.B.Boraston (2007). The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase. J Mol Biol, 368, 1215-1222. PubMed id: 17397864 DOI: 10.1016/j.jmb.2007.02.083
09-Mar-07     Release date:   08-May-07    
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Protein chains
Pfam   ArchSchema ?
O68975  (O68975_YEREN) -  Exopolygalacturonase
601 a.a.
571 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     polygalacturonase activity     1 term  


DOI no: 10.1016/j.jmb.2007.02.083 J Mol Biol 368:1215-1222 (2007)
PubMed id: 17397864  
The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase.
D.W.Abbott, A.B.Boraston.
Family 28 glycoside hydrolases (polygalacturonases) are found in organisms across the plant, fungal and bacterial kingdoms, where they are central to diverse biological functions such as fruit ripening, biomass recycling and plant pathogenesis. The structures of several polygalacturonases have been reported; however, all of these enzymes utilize an endo-mode of digestion, which generates a spectrum of oligosaccharide products with varying degrees of polymerization. The structure of a complementary exo-acting polygalacturonase and an accompanying explanation of the molecular determinants for its specialized activity have been noticeably lacking. We present the structure of an exopolygalacturonase from Yersinia enterocolitica, YeGH28 in a native form (solved to 2.19 A resolution) and a digalacturonic acid product complex (solved to 2.10 A resolution). The activity of YeGH28 is due to inserted stretches of amino acid residues that transform the active site from the open-ended channel observed in the endopolygalacturonases to a closed pocket that restricts the enzyme to the exclusive attack of the non-reducing end of oligogalacturonide substrates. In addition, YeGH28 possesses a fused FN3 domain with unknown function, the first such structure described in pectin active enzymes.
  Selected figure(s)  
Figure 1.
Figure 2.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 368, 1215-1222) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21161225 J.A.Mertens, and M.J.Bowman (2011).
Expression and characterization of fifteen Rhizopus oryzae 99-880 polygalacturonase enzymes in Pichia pastoris.
  Curr Microbiol, 62, 1173-1178.  
20824208 J.T.Noel, N.Arrach, A.Alagely, M.McClelland, and M.Teplitski (2010).
Specific responses of Salmonella enterica to tomato varieties and fruit ripeness identified by in vivo expression technology.
  PLoS One, 5, e12406.  
18430740 C.Creze, S.Castang, E.Derivery, R.Haser, N.Hugouvieux-Cotte-Pattat, V.E.Shevchik, and P.Gouet (2008).
The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate.
  J Biol Chem, 283, 18260-18268.
PDB codes: 3b4n 3b8y 3b90
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
  18607098 P.B.Vordtriede, and M.D.Yoder (2008).
Crystallization, X-ray diffraction analysis and preliminary structure determination of the polygalacturonase PehA from Agrobacterium vitis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 645-647.  
18704748 Z.Xiao, S.Wang, H.Bergeron, J.Zhang, and P.C.Lau (2008).
A flax-retting endopolygalacturonase-encoding gene from Rhizopus oryzae.
  Antonie Van Leeuwenhoek, 94, 563-571.  
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