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PDBsum entry 2uve

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2uve
Jmol
Contents
Protein chains
571 a.a. *
Ligands
SO4 ×19
ACT
Metals
_NI ×9
Waters ×463
* Residue conservation analysis
PDB id:
2uve
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
Resolution:
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
Date:
09-Mar-07     Release date:   08-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O68975  (O68975_YEREN) -  Exopolygalacturonase
Seq:
Struc:
 
Seq:
Struc:
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     metal ion binding     2 terms  

 

 
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.
 
  ABSTRACT  
 
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.  
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.