PDBsum entry 2v8i

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protein metals links
Lyase PDB id
Protein chain
543 a.a. *
IOD ×51
Waters ×759
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Structure of a family 2 pectate lyase in a native form
Structure: Pectate lyase. Chain: a. Engineered: yes
Source: Yersinia enterocolitica. Organism_taxid: 630. Expressed in: escherichia coli. Expression_system_taxid: 562
1.50Å     R-factor:   0.223     R-free:   0.243
Authors: D.W.Abbott,A.B.Boraston
Key ref:
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. PubMed id: 17881361 DOI: 10.1074/jbc.M705511200
08-Aug-07     Release date:   18-Sep-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
A1JSS8  (A1JSS8_YERE8) -  Periplasmic pectate lyase
572 a.a.
543 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     pectin catabolic process   1 term 
  Biochemical function     lyase activity     3 terms  


DOI no: 10.1074/jbc.M705511200 J Biol Chem 282:35328-35336 (2007)
PubMed id: 17881361  
A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination.
D.W.Abbott, A.B.Boraston.
The family 2 pectate lyase from Yersinia enterocolitica (YePL2A), solved to 1.5A, reveals it to be the first prokaryotic protein reported to display the rare (alpha/alpha)(7) barrel fold. In addition to its apo form, we have also determined the structure of a metal-bound form of YePL2A (to 2.0A) and a trigalacturonic acid-bound substrate complex (to 2.1A) Although its fold is rare, the catalytic center of YePL2A can be superimposed with structurally unrelated families, underlining the conserved catalytic amino acid architecture of the beta-elimination mechanism. In addition to its overall structure, YePL2A also has two other unique features: 1) it utilizes a metal atom other than calcium for catalysis, and 2) its Brønstead base is in an alternate conformation and directly interacts with the uronate group of the substrate.
  Selected figure(s)  
Figure 4.
FIGURE 4. The YePL2A metal coordination pocket and alternate conformations of YePL2A. A, wall-eyed stereo view of the metal coordination site. The metal is refined as a Mn^2+ ion and colored silver. Amino acids involved in coordination: His^109, Glu^130, and His^172 are displayed in stick representation, and the three waters are shown as spheres (red). The weighted maximum-likelihood (26)/ [A] (47) 2F[obs] - F[calc] map is contoured to 1.0 (0.33 e^-/Å^3). B, the metal (yellow) and trigalUA (red) complexes of YePL2A are superimposed and rendered in a ribbon format. C, solvent-accessible surfaces models of the metal bound (cyan) and trigalUA bound (gray) forms of YePL2A. The catalytic machinery of the substrate complex is colored in blue.
Figure 5.
FIGURE 5. Structural conservation of the active sites within pectate lyases displaying diverse folds. The unique folds for three different pectate lyase families are shown in panels A-C. A,( / )[6] toroid (Protein Data Bank code 1GXO). B,( / )[7] barrel (Protein Data Bank code 2V8I). C, β-helix (Protein Data Bank code 2EWE). D, a general Ca^2+ assisted β-elimination mechanism used by pectate lyases. E, overlay of the catalytic residues from the enzymes in A-C displayed in wall-eyed stereo. EcPL1 is colored in green, YePL2A in yellow, and CjPL10 in cyan. Calcium ions for EcPL1 and CjPL10 are rendered in magenta and purple, respectively. The distinct metal-binding site of YePL2A is integrated by overlaying His^109, Glu^130, and His^172 (also in yellow), and Mn^2+ (silver) from the metal-bound structure (2V8I). The substrates are trimmed to the -1 and +1 residues for clarity.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 35328-35336) copyright 2007.  
  Figures were selected by an automated process.  

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.  
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
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