PDBsum entry 1qjv

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Hydrolase (aspartyl esterase) PDB id
Protein chains
342 a.a. *
_CL ×2
Waters ×618
* Residue conservation analysis
PDB id:
Name: Hydrolase (aspartyl esterase)
Title: Pectin methylesterase pema from erwinia chrysanthemi
Structure: Pectin methylesterase. Chain: a, b. Fragment: mature enzyme (residues 25-366). Synonym: pectinesterase. Engineered: yes
Source: Erwinia chrysanthemi. Organism_taxid: 556. Strain: b374. Cellular_location: extracellular. Gene: pema. Expressed in: bacillus subtilis. Expression_system_taxid: 1423. Other_details: the expression system strain is from the uk national collection of plant pathogenic bacteria (ncppb)
2.37Å     R-factor:   0.170     R-free:   0.212
Authors: J.Jenkins,O.Mayans,D.Smith,K.Worboys,R.Pickersgill
Key ref:
J.Jenkins et al. (2001). Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site. J Mol Biol, 305, 951-960. PubMed id: 11162105 DOI: 10.1006/jmbi.2000.4324
05-Jul-99     Release date:   14-Jul-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0C1A8  (PMEA_ERWCH) -  Pectinesterase A
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.  - Pectinesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Pectin + n H2O = n methanol + pectate
+ 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  


DOI no: 10.1006/jmbi.2000.4324 J Mol Biol 305:951-960 (2001)
PubMed id: 11162105  
Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site.
J.Jenkins, O.Mayans, D.Smith, K.Worboys, R.W.Pickersgill.
Most structures of neutral lipases and esterases have been found to adopt the common alpha/beta hydrolase fold and contain a catalytic Ser-His-Asp triad. Some variation occurs in both the overall protein fold and in the location of the catalytic triad, and in some enzymes the role of the aspartate residue is replaced by a main-chain carbonyl oxygen atom. Here, we report the crystal structure of pectin methylesterase that has neither the common alpha/beta hydrolase fold nor the common catalytic triad. The structure of the Erwinia chrysanthemi enzyme was solved by multiple isomorphous replacement and refined at 2.4 A to a conventional crystallographic R-factor of 17.9 % (R(free) 21.1 %). This is the first structure of a pectin methylesterase and reveals the enzyme to comprise a right-handed parallel beta-helix as seen in the pectinolytic enzymes pectate lyase, pectin lyase, polygalacturonase and rhamnogalacturonase, and unlike the alpha/beta hydrolase fold of rhamnogalacturonan acetylesterase with which it shares esterase activity. Pectin methylesterase has no significant sequence similarity with any protein of known structure. Sequence conservation among the pectin methylesterases has been mapped onto the structure and reveals that the active site comprises two aspartate residues and an arginine residue. These proposed catalytic residues, located on the solvent-accessible surface of the parallel beta-helix and in a cleft formed by external loops, are at a location similar to that of the active site and substrate-binding cleft of pectate lyase. The structure of pectin methylesterase is an example of a new family of esterases.
  Selected figure(s)  
Figure 1.
Figure 1. The substrate for pectin methylesterase is the methylated a-(1-4)-linked Image -galacturonosyl residue region of the pectin molecule. A fully methylated trisaccharide is shown for illustration. Pectin methylesterase catalyses the hydrolysis of the ester bond indicated by the arrow.
Figure 5.
Figure 5. Stereo view of pectin methylesterase looking down onto the putative substrate-binding cleft. The contact surface is coloured by the nearest atom: oxygen red, nitrogen blue, aliphatic carbon gold and sulphur yellow. All side-chain atoms of phenylalanine, tyrosine and tryptophan are green. Aromatics (green) can be seen to cluster in the same cleft in which conservation is high (Figure 4). This Figure was prepared using the program MOLMOL. [45]
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 305, 951-960) copyright 2001.  
  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.  
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.  
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
17581207 R.Barderas, J.García-Sellés, G.Salamanca, C.Colás, D.Barber, R.Rodríguez, and M.Villalba (2007).
A pectin methylesterase as an allergenic marker for the sensitization to Russian thistle (Salsola kali) pollen.
  Clin Exp Allergy, 37, 1111-1119.  
15968068 S.A.Douthit, M.Dlakic, D.E.Ohman, and M.J.Franklin (2005).
Epimerase active domain of Pseudomonas aeruginosa AlgG, a protein that contains a right-handed beta-helix.
  J Bacteriol, 187, 4573-4583.  
14557261 F.Vincent, D.Yates, E.Garman, G.J.Davies, and J.A.Brannigan (2004).
The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.
  J Biol Chem, 279, 2809-2816.
PDB codes: 1un7 2vhl
14670977 J.Jenkins, V.E.Shevchik, N.Hugouvieux-Cotte-Pattat, and R.W.Pickersgill (2004).
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.
  J Biol Chem, 279, 9139-9145.
PDB code: 1ru4
12962629 A.M.Larsson, R.Andersson, J.Ståhlberg, L.Kenne, and T.A.Jones (2003).
Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.
  Structure, 11, 1111-1121.
PDB codes: 1ogm 1ogo
12744465 O.Valette-Collet, A.Cimerman, P.Reignault, C.Levis, and M.Boccara (2003).
Disruption of Botrytis cinerea pectin methylesterase gene Bcpme1 reduces virulence on several host plants.
  Mol Plant Microbe Interact, 16, 360-367.  
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.  
12015881 L.Cowen, P.Bradley, M.Menke, J.King, and B.Berger (2002).
Predicting the beta-helix fold from protein sequence data.
  J Comput Biol, 9, 261-276.  
11544130 F.Micheli (2001).
Pectin methylesterases: cell wall enzymes with important roles in plant physiology.
  Trends Plant Sci, 6, 414-419.  
  11493601 G.Michel, L.Chantalat, E.Fanchon, B.Henrissat, B.Kloareg, and O.Dideberg (2001).
The iota-carrageenase of Alteromonas fortis. A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide.
  J Biol Chem, 276, 40202-40209.
PDB code: 1h80
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.