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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
3b8y
Jmol
Contents
Protein chains
304 a.a. *
Ligands
ADA-ADA-ADA-ADA ×2
Metals
_CA
_ZN
Waters ×171
* Residue conservation analysis
PDB id:
3b8y
Name: Lyase
Title: Crystal structure of pectate lyase peli from erwinia chrysanthemi in complex with tetragalacturonic acid
Structure: Endo-pectate lyase. Chain: a, b. Engineered: yes
Source: Erwinia chrysanthemi. Organism_taxid: 556. Gene: peli. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.30Å     R-factor:   0.198     R-free:   0.253
Authors: C.Creze,S.Castang,E.Derivery,R.Haser,V.Shevchik,P.Gouet
Key ref:
C.Creze et al. (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. PubMed id: 18430740 DOI: 10.1074/jbc.M709931200
Date:
02-Nov-07     Release date:   29-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O50325  (O50325_ERWCH) -  Endo-pectate lyase (Precursor)
Seq:
Struc:
344 a.a.
304 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.4.2.2.2  - Pectate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
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 
  Biochemical function     pectate lyase activity     1 term  

 

 
DOI no: 10.1074/jbc.M709931200 J Biol Chem 283:18260-18268 (2008)
PubMed id: 18430740  
 
 
The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate.
C.Creze, S.Castang, E.Derivery, R.Haser, N.Hugouvieux-Cotte-Pattat, V.E.Shevchik, P.Gouet.
 
  ABSTRACT  
 
The crystallographic structure of the family 3 polysaccharide lyase (PL-3) PelI from Erwinia chrysanthemi has been solved to 1.45 A resolution. It consists of an N-terminal domain harboring a fibronectin type III fold linked to a catalytic domain displaying a parallel beta-helix topology. The N-terminal domain is located away from the active site and is not involved in the catalytic process. After secretion in planta, the two domains are separated by E. chrysanthemi proteases. This event turns on the hypersensitive response of the host. The structure of the single catalytic domain determined to 2.1 A resolution shows that the domain separation unveils a "Velcro"-like motif of asparagines, which might be recognized by a plant receptor. The structure of PelI in complex with its substrate, a tetragalacturonate, has been solved to 2.3 A resolution. The sugar binds from subsites -2 to +2 in one monomer of the asymmetric unit, although it lies on subsites -1 to +3 in the other. These two "Michaelis complexes" have never been observed simultaneously before and are consistent with the dual mode of bond cleavage in this substrate. The bound sugar adopts a mixed 2(1) and 3(1) helical conformation similar to that reported in inactive mutants from families PL-1 and PL-10. However, our study suggests that the catalytic base in PelI is not a conventional arginine but a lysine as proposed in family PL-9.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Structural alignment of the catalytic domain of PelI. A, superimposition of the catalytic domain of PelI (blue) with Pel15 (red) (Protein Data Bank code 1EE6 [PDB] ) and PelC (green) (Protein Data Bank code 2EWE). Bound calcium ions are shown in PelI, Pel15, and PelC with blue, red, and green spheres, respectively. The bound sugar in PelC is shown in yellow. The disordered linker in PelI is shown by a dashed line. B, structure-based sequence alignment with secondary structure elements. Top, red and blue triangles indicate the putative catalytic residue of PelI and PelC, respectively. Bottom, green numbers, red stars, and blue circles indicate PelI disulfide bridges, residues at the interdomain interface (contact distances <3.2 Å), and residues coordinated to a Ca^2+ ion, respectively.
Figure 3.
FIGURE 3. Interactions between the tetrasaccharide and the protein. A, in molecule A. B, in molecule B. The moiety Ada1 is at the reducing end (A1 or B1), and the moiety Ada4 is at the non-reducing end (A4 or B4). A yellow arrow symbolizes the proton abstraction at the C[5] atom.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 18260-18268) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21470403 H.Wang, L.Fu, and X.Zhang (2011).
Comparison of expression, purification and characterization of a new pectate lyase from Phytophthora capsici using two different methods.
  BMC Biotechnol, 11, 32.  
21192002 Y.K.Liu, Y.L.Lin, C.H.Chen, C.M.Lin, K.L.Ma, F.H.Chou, J.S.Tsai, H.Y.Lin, F.R.Chen, T.L.Cheng, C.C.Chang, and K.W.Liao (2011).
A unique and potent protein binding nature of liposome containing polyethylenimine and polyethylene glycol: a nondisplaceable property.
  Biotechnol Bioeng, 108, 1318-1327.  
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
20852644 S.L.Reichow, K.V.Korotkov, W.G.Hol, and T.Gonen (2010).
Structure of the cholera toxin secretion channel in its closed state.
  Nat Struct Mol Biol, 17, 1226-1232.  
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.