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PDBsum entry 2nt9

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2nt9
Jmol
Contents
Protein chains
342 a.a. *
Ligands
ADA-M8C-M8C-M8C-
M8C-ADA
×2
Waters ×809
* Residue conservation analysis
PDB id:
2nt9
Name: Hydrolase
Title: Crystal structure of pectin methylesterase d178a mutant in c with hexasaccharide iv
Structure: Pectinesterase a. Chain: a, b. Synonym: pectin methylesterase a, pe a. Engineered: yes. Mutation: yes
Source: Erwinia chrysanthemi. Organism_taxid: 198628. Strain: 3937. Gene: pema, pem. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.187     R-free:   0.210
Authors: M.Fries,K.Brocklehurst,V.E.Shevchik,R.W.Pickersgill
Key ref:
M.Fries et al. (2007). Molecular basis of the activity of the phytopathogen pectin methylesterase. EMBO J, 26, 3879-3887. PubMed id: 17717531 DOI: 10.1038/sj.emboj.7601816
Date:
07-Nov-06     Release date:   18-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0C1A9  (PMEA_DICD3) -  Pectinesterase A
Seq:
Struc:
366 a.a.
342 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.3.1.1.11  - Pectinesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Pectin + n H2O = n methanol + pectate
Pectin
+ n H(2)O
= n methanol
+ pectate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     cell wall organization   3 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7601816 EMBO J 26:3879-3887 (2007)
PubMed id: 17717531  
 
 
Molecular basis of the activity of the phytopathogen pectin methylesterase.
M.Fries, J.Ihrig, K.Brocklehurst, V.E.Shevchik, R.W.Pickersgill.
 
  ABSTRACT  
 
We provide a mechanism for the activity of pectin methylesterase (PME), the enzyme that catalyses the essential first step in bacterial invasion of plant tissues. The complexes formed in the crystal using specifically methylated pectins, together with kinetic measurements of directed mutants, provide clear insights at atomic resolution into the specificity and the processive action of the Erwinia chrysanthemi enzyme. Product complexes provide additional snapshots along the reaction coordinate. We previously revealed that PME is a novel aspartic-esterase possessing parallel beta-helix architecture and now show that the two conserved aspartates are the nucleophile and general acid-base in the mechanism, respectively. Other conserved residues at the catalytic centre are shown to be essential for substrate binding or transition state stabilisation. The preferential binding of methylated sugar residues upstream of the catalytic site, and demethylated residues downstream, drives the enzyme along the pectin molecule and accounts for the sequential pattern of demethylation produced by both bacterial and plant PMEs.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Enzyme–substrate interactions in detail. (A) Stereo-view of the stick model of the Michaelis complex formed using compound II overlaid with maximum likelihood/ [A] weighted 2F[o]-F[c] syntheses contoured at 1.5 and (B) schematic diagram showing the interactions involved. (B) was produced using LIGPLOT (Wallace et al, 1995).
Figure 4.
Figure 4 The proposed mechanism of PME based on the crystal structures and kinetic analyses of directed mutants.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 3879-3887) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20858733 M.Hothorn, W.Van den Ende, W.Lammens, V.Rybin, and K.Scheffzek (2010).
Structural insights into the pH-controlled targeting of plant cell-wall invertase by a specific inhibitor protein.
  Proc Natl Acad Sci U S A, 107, 17427-17432.
PDB code: 2xqr
20441763 P.J.Edwards, M.Kakubayashi, R.Dykstra, S.M.Pascal, and M.A.Williams (2010).
Rheo-NMR studies of an enzymatic reaction: evidence of a shear-stable macromolecular system.
  Biophys J, 98, 1986-1994.  
19820151 C.Chakiath, M.J.Lyons, R.E.Kozak, and C.S.Laufer (2009).
Thermal Stabilization of Erwinia chrysanthemi pectin methylesterase a for application in a sugar beet pulp biorefinery.
  Appl Environ Microbiol, 75, 7343-7349.  
19333997 J.Øbro, I.Sørensen, P.Derkx, C.T.Madsen, M.Drews, M.Willer, J.D.Mikkelsen, and W.G.Willats (2009).
High-throughput screening of Erwinia chrysanthemi pectin methylesterase variants using carbohydrate microarrays.
  Proteomics, 9, 1861-1868.  
18936961 S.Dedeurwaerder, L.Menu-Bouaouiche, A.Mareck, P.Lerouge, and F.Guerineau (2009).
Activity of an atypical Arabidopsis thaliana pectin methylesterase.
  Planta, 229, 311-321.  
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
18643934 Y.Ferrandez, and G.Condemine (2008).
Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.
  Mol Microbiol, 69, 1349-1357.  
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 code is shown on the right.