PDBsum entry 1o8d

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protein metals links
Hydrolase PDB id
Jmol PyMol
Protein chain
353 a.a. *
Waters ×145
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Pectate lyasE C from erwinia chrysanthemi at ph 11.2 with 5mm ca2+
Structure: Pectate lyasE C. Chain: a. Engineered: yes
Source: Erwinia chrysanthemi. Organism_taxid: 556. Expressed in: escherichia coli. Expression_system_taxid: 562
2.2Å     R-factor:   0.180     R-free:   0.218
Authors: S.R.Herron,F.A.Jurnak
Key ref:
S.R.Herron et al. (2003). Characterization and implications of Ca2+ binding to pectate lyase C. J Biol Chem, 278, 12271-12277. PubMed id: 12540845 DOI: 10.1074/jbc.M209306200
27-Nov-02     Release date:   30-Jan-03    
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Protein chain
Pfam   ArchSchema ?
P11073  (PLYC_ERWCH) -  Pectate lyase C
375 a.a.
353 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Pectate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Pectin and Pectate Lyases
      Reaction: Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     pathogenesis   2 terms 
  Biochemical function     lyase activity     3 terms  


DOI no: 10.1074/jbc.M209306200 J Biol Chem 278:12271-12277 (2003)
PubMed id: 12540845  
Characterization and implications of Ca2+ binding to pectate lyase C.
S.R.Herron, R.D.Scavetta, M.Garrett, M.Legner, F.Jurnak.
Ca(2+) is essential for in vitro activity of Erwinia chrysanthemi pectate lyase C (PelC). Crystallographic analyses of 11 PelC-Ca(2+) complexes, formed at pH 4.5, 9.5, and 11.2 under varying Ca(2+) concentrations, have been solved and refined at a resolution of 2.2 A. The Ca(2+) site represents a new motif for Ca(2+), consisting primarily of beta-turns and beta-strands. The principal differences between PelC and the PelC-Ca(2+) structures at all pH values are the side-chain conformations of Asp-129 and Glu-166 as well as the occupancies of four water molecules. According to calculations of pK(a) values, the presence of Ca(2+) and associated structural changes lower the pK(a) of Arg-218, the amino acid responsible for proton abstraction during catalysis. The Ca(2+) affinity for PelC is weak, as the K(d) was estimated to be 0.132 (+/-0.004) mm at pH 9.5, 1.09 (+/-0.29) mm at pH 11.2, and 5.84 (+/-0.41) mm at pH 4.5 from x-ray diffraction studies and 0.133 (+/-0.045) mm at pH 9.5 from intrinsic tryptophan fluorescence measurements. Given the pH dependence of Ca(2+) affinity, PelC activity at pH 4.5 has been reexamined. At saturating Ca(2+) concentrations, PelC activity increases 10-fold at pH 4.5 but is less than 1% of maximal activity at pH 9.5. Taken together, the studies suggest that the primary Ca(2+) ion in PelC has multiple functions.
  Selected figure(s)  
Figure 1.
Fig. 1. Plot of the slow exchange of the solution bathing PelC crystals. The concentrations of ammonium sulfate ( ) and polyethylene glycol 8000 ( ) in the 1-ml drop containing a PelC crystal are plotted as a function of time.
Figure 6.
Fig. 6. Stereoviews of three types of Ca^2+ binding motifs. A, the Ca^2+ region of -lactalbumin exemplifies the continuous helix-loop-helix Ca^2+ binding motif, which is associated with tight binding. B, the Ca^2+ region of phospholipase A2 typifies the discontinuous helix-loop-helix Ca^2+ binding motif. C, the -turn/ -strand Ca^2+ binding motif of PelC exhibits weak binding affinity. In all figures, the polypeptide backbone of the protein is represented as a green ribbon, the Ca^2+ ions as yellow spheres, the oxygen atoms as red rods, and a disulfide bridge as a yellow bar.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 12271-12277) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
18843399 C.Trujillo, A.M.Lamsabhi, O.Mó, M.Yáñez, and J.Y.Salpin (2008).
Interaction of Ca2+ with uracil and its thio derivatives in the gas phase.
  Org Biomol Chem, 6, 3695-3702.  
18317750 Z.Xiao, J.Boyd, S.Grosse, M.Beauchemin, E.Coupe, and P.C.Lau (2008).
Mining Xanthomonas and Streptomyces genomes for new pectinase-encoding sequences and their heterologous expression in Escherichia coli.
  Appl Microbiol Biotechnol, 78, 973-981.  
15668006 E.Laasik, M.Ojarand, M.Pajunen, H.Savilahti, and A.Mäe (2005).
Novel mutants of Erwinia carotovora subsp. carotovora defective in the production of plant cell wall degrading enzymes generated by Mu transpososome-mediated insertion mutagenesis.
  FEMS Microbiol Lett, 243, 93-99.  
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.