spacer
spacer

PDBsum entry 1gq8

Go to PDB code: 
protein ligands links
Hydrolase PDB id
1gq8
Jmol
Contents
Protein chain
319 a.a. *
Ligands
CAC ×2
Waters ×345
* Residue conservation analysis
PDB id:
1gq8
Name: Hydrolase
Title: Pectin methylesterase from carrot
Structure: Pectinesterase. Chain: a. Synonym: pectin methylesterase, pe. Ec: 3.1.1.11
Source: Daucus carota. Carrot. Organism_taxid: 4039. Organ: ripe roots
Resolution:
1.75Å     R-factor:   0.181     R-free:   0.193
Authors: K.Johansson,M.El-Ahmad,R.Friemann,H.Jornvall,O.Markovic, H.Eklund
Key ref:
K.Johansson et al. (2002). Crystal structure of plant pectin methylesterase. FEBS Lett, 514, 243-249. PubMed id: 11943159 DOI: 10.1016/S0014-5793(02)02372-4
Date:
20-Nov-01     Release date:   18-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P83218  (PME_DAUCA) -  Pectinesterase
Seq:
Struc:
319 a.a.
319 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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: 10.1016/S0014-5793(02)02372-4 FEBS Lett 514:243-249 (2002)
PubMed id: 11943159  
 
 
Crystal structure of plant pectin methylesterase.
K.Johansson, M.El-Ahmad, R.Friemann, H.Jörnvall, O.Markovic, H.Eklund.
 
  ABSTRACT  
 
Pectin is a principal component in the primary cell wall of plants. During cell development, pectin is modified by pectin methylesterases to give different properties to the cell wall. This report describes the first crystal structure of a plant pectin methylesterase. The beta-helical structure embodies a central cleft, lined by several aromatic residues, that has been deduced to be suitable for pectin binding. The active site is found at the center of this cleft where Asp157 is suggested to act as the nucleophile, Asp136 as an acid/base and Gln113/Gln135 to form an anion hole to stabilize the transition state.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereo figures of the electron density maps at 1.75 Å resolution. A: Electron density map of the PB2 sheet (2F[o]−F[c]) contoured at 1σ after ARP/wARP modeling and initial refinement. Notice the stacking of three internal cysteines at the left of the figure. B: In the final electron density map (2F[o]−F[c] contoured at 1σ), the cyclic N-terminal pyroglutamate residue was visible. Figures were made by O-plot [35].
Figure 3.
Fig. 3. The active site. The substrate, a methylesterified Image -galactosiduronic acid unit, is modeled in the active site. Arg225 is hydrogen-bonded to Asp157, which is suitably positioned for nucleophilic attack on the carboxymethyl carbon, while Asp136 would act as an acid/base during catalysis. The two glutamine residues, Gln113 and Gln135, could form an anion hole for stabilization of the negatively charged tetrahedral intermediate.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2002, 514, 243-249) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21259289 P.Li, B.Feng, H.Wang, P.W.Tooley, and X.Zhang (2011).
Isolation of nine Phytophthora capsici pectin methylesterase genes which are differentially expressed in various plant species.
  J Basic Microbiol, 51, 61-70.  
20491902 G.Salamanca, R.Rodríguez, J.Quiralte, C.Moreno, C.Y.Pascual, D.Barber, and M.Villalba (2010).
Pectin methylesterases of pollen tissue, a major allergen in olive tree.
  FEBS J, 277, 2729-2739.  
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.  
19357434 D.Mbéguié-A-Mbéguié, O.Hubert, F.C.Baurens, T.Matsumoto, M.Chillet, B.Fils-Lycaon, and S.Sidibé-Bocs (2009).
Expression patterns of cell wall-modifying genes from banana during fruit ripening and in relationship with finger drop.
  J Exp Bot, 60, 2021-2034.  
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.  
17932919 M.A.Ciardiello, R.D'Avino, A.Amoresano, L.Tuppo, A.Carpentieri, V.Carratore, M.Tamburrini, A.Giovane, P.Pucci, and L.Camardella (2008).
The peculiar structural features of kiwi fruit pectin methylesterase: amino acid sequence, oligosaccharides structure, and modeling of the interaction with its natural proteinaceous inhibitor.
  Proteins, 71, 195-206.  
17881361 D.W.Abbott, and A.B.Boraston (2007).
A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination.
  J Biol Chem, 282, 35328-35336.
PDB codes: 2v8i 2v8j 2v8k
17717531 M.Fries, J.Ihrig, K.Brocklehurst, V.E.Shevchik, and R.W.Pickersgill (2007).
Molecular basis of the activity of the phytopathogen pectin methylesterase.
  EMBO J, 26, 3879-3887.
PDB codes: 2nsp 2nst 2nt6 2nt9 2ntb 2ntp 2ntq
16622707 R.Louvet, E.Cavel, L.Gutierrez, S.Guénin, D.Roger, F.Gillet, F.Guerineau, and J.Pelloux (2006).
Comprehensive expression profiling of the pectin methylesterase gene family during silique development in Arabidopsis thaliana.
  Planta, 224, 782-791.  
  15284866 M.G.Francki, and D.J.Mullan (2004).
Application of comparative genomics to narrow-leafed lupin (Lupinus angustifolius L.) using sequence information from soybean and Arabidopsis.
  Genome, 47, 623-632.  
14635125 R.D'Avino, L.Camardella, T.M.Christensen, A.Giovane, and L.Servillo (2003).
Tomato pectin methylesterase: modeling, fluorescence, and inhibitor interaction studies-comparison with the bacterial (Erwinia chrysanthemi) enzyme.
  Proteins, 53, 830-839.  
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.