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PDBsum entry 1jta

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Lyase PDB id
1jta
Jmol
Contents
Protein chain
361 a.a. *
Ligands
SO4
Waters ×244
* Residue conservation analysis
PDB id:
1jta
Name: Lyase
Title: Crystal structure of pectate lyase a (c2 form)
Structure: Pectate lyase a. Chain: a. Engineered: yes
Source: Erwinia chrysanthemi. Organism_taxid: 556. Strain: ec16. Gene: pela. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.181     R-free:   0.225
Authors: L.M.Thomas,C.N.Doan,R.L.Oliver,M.D.Yoder
Key ref:
L.M.Thomas et al. (2002). Structure of pectate lyase A: comparison to other isoforms. Acta Crystallogr D Biol Crystallogr, 58, 1008-1015. PubMed id: 12037303 DOI: 10.1107/S0907444902005851
Date:
20-Aug-01     Release date:   19-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C1A2  (PLYA_ERWCH) -  Pectate lyase A
Seq:
Struc:
393 a.a.
361 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 
  Biological process     pectin catabolic process   1 term 
  Biochemical function     lyase activity     3 terms  

 

 
DOI no: 10.1107/S0907444902005851 Acta Crystallogr D Biol Crystallogr 58:1008-1015 (2002)
PubMed id: 12037303  
 
 
Structure of pectate lyase A: comparison to other isoforms.
L.M.Thomas, C.N.Doan, R.L.Oliver, M.D.Yoder.
 
  ABSTRACT  
 
Pectate lyase A is a virulence factor secreted by the plant-pathogenic bacteria Erwinia chrysanthemi. The enzyme cleaves the glycosidic bond of pectate polymers by a calcium-dependent beta-elimination mechanism. The crystal structure of pectate lyase A from E. chrysanthemi EC16 has been determined in two crystal forms, monoclinic C2 to 1.8 A and rhombohedral R3 to 2.1 A. The protein structure is compared with two other pectate lyase isoforms from E. chrysanthemi EC16, pectate lyase C and pectate lyase E. Pectate lyase A is unique as it is the only acidic pectate lyase and has end products that are significantly more varied in length in comparison to those of the other four major pectate lyase isozymes. Differences and similarities in polypeptide trace, size and volume of the active-site groove and surface electrostatics are discussed.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Structure of PelA from E. chrysanthemi. (a) A ribbons-style representation with the three parallel -sheets of the parallel -helix shown in different colors: yellow for PB1, blue for PB2 and red for PB3. The two -ribbons not participating in the parallel -helix are shown in green. The disulfide bond is drawn as an orange thunderbolt. The N- and C-termini are labeled `N' and `C', respectively. (b) Stereo diagram of the C^ chain trace of PelA in the C2 crystal form. Residue numbers throughout the molecule are indicated.
Figure 5.
Figure 5 Active-site groove of PelA, PelC and PelE. The masked active-site groove is displayed in cyan, with the C^ chain trace of the proteins in red. (a) PelA, (b) PelC, (c) PelE.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1008-1015) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19452560 K.L.Hindle, J.Bella, and S.C.Lovell (2009).
Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.
  Proteins, 77, 342-358.  
18430740 C.Creze, S.Castang, E.Derivery, R.Haser, N.Hugouvieux-Cotte-Pattat, V.E.Shevchik, and P.Gouet (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.
PDB codes: 3b4n 3b8y 3b90
17947240 A.Ochiai, T.Itoh, Y.Maruyama, A.Kawamata, B.Mikami, W.Hashimoto, and K.Murata (2007).
A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER.
  J Biol Chem, 282, 37134-37145.
PDB codes: 2z8r 2z8s
15539389 E.W.Czerwinski, T.Midoro-Horiuti, M.A.White, E.G.Brooks, and R.M.Goldblum (2005).
Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core.
  J Biol Chem, 280, 3740-3746.
PDB code: 1pxz
15264254 E.F.Pettersen, T.D.Goddard, C.C.Huang, G.S.Couch, D.M.Greenblatt, E.C.Meng, and T.E.Ferrin (2004).
UCSF Chimera--a visualization system for exploratory research and analysis.
  J Comput Chem, 25, 1605-1612.  
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.