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PDBsum entry 1air

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protein ligands links
Pectate cleavage PDB id
1air
Jmol
Contents
Protein chain
352 a.a. *
Ligands
SO4 ×2
Waters ×384
* Residue conservation analysis
PDB id:
1air
Name: Pectate cleavage
Title: Pectate lyasE C from erwinia chrysanthemi (ec16) to a resolution of 2.2 angstroms with 128 waters
Structure: Pectate lyasE C. Chain: a. Synonym: pelc. Ec: 4.2.2.2
Source: Erwinia chrysanthemi. Organism_taxid: 556. Strain: ec16. Cellular_location: extracellular. Plasmid: hb101
Resolution:
2.20Å     R-factor:   0.172     R-free:   0.223
Authors: S.E.Lietzke,R.D.Scavetta,M.D.Yoder,F.A.Jurnak
Key ref: S.E.Lietzke et al. (1996). The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution. Plant Physiol, 111, 73-92. PubMed id: 12226275
Date:
24-Apr-97     Release date:   16-Jun-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11073  (PLYC_ERWCH) -  Pectate lyase C
Seq:
Struc:
375 a.a.
352 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     pathogenesis   2 terms 
  Biochemical function     lyase activity     3 terms  

 

 
Plant Physiol 111:73-92 (1996)
PubMed id: 12226275  
 
 
The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution.
S.E.Lietzke, R.D.Scavetta, M.D.Yoder, F.Jurnak.
 
  ABSTRACT  
 
The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the enterobacteria Erwinia chrysanthemi has been refined by molecular dynamics techniques to a resolution of 2.2 A and an R factor (an agreement factor between observed structure factor amplitudes) of 16.1%. The final model consists of all 355 amino acids and 157 water molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.721[deg] for bond angles. The structure of PelE bound to a lanthanum ion, which inhibits the enzymatic activity, has also been refined and compared to the metal-free protein. In addition, the structures of pectate lyase C (PelC) in the presence and absence of a lutetium ion have been refined further using an improved algorithm for identifying waters and other solvent molecules. The two putative active site regions of PelE have been compared to those in the refined structure of PelC. The analysis of the atomic details of PelE and PelC in the presence and absence of lanthanide ions provides insight into the enzymatic mechanism of pectate lyases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
18156340 Z.Xiao, H.Bergeron, S.Grosse, M.Beauchemin, M.L.Garron, D.Shaya, T.Sulea, M.Cygler, and P.C.Lau (2008).
Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment.
  Appl Environ Microbiol, 74, 1183-1189.
PDB codes: 2qx3 2qxz 2qy1
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
12897238 N.Ferguson, J.Berriman, M.Petrovich, T.D.Sharpe, J.T.Finch, and A.R.Fersht (2003).
Rapid amyloid fiber formation from the fast-folding WW domain FBP28.
  Proc Natl Acad Sci U S A, 100, 9814-9819.  
12554946 T.Nakaniwa, T.Tada, K.Ishii, M.Takao, T.Sakai, and K.Nishimura (2003).
Crystallization and preliminary X-ray analysis of a thermostable pectate lyase PL 47 from Bacillus sp. TS 47.
  Acta Crystallogr D Biol Crystallogr, 59, 341-342.  
12377130 H.Jing, J.Takagi, J.H.Liu, S.Lindgren, R.G.Zhang, A.Joachimiak, J.H.Wang, and T.A.Springer (2002).
Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins.
  Structure, 10, 1453-1464.
PDB code: 1l0q
11914504 M.A.McDonough, C.Ryttersgaard, M.E.Bjørnvad, L.Lo Leggio, M.Schülein, S.O.Schrøder Glad, and S.Larsen (2002).
Crystallization and preliminary X-ray characterization of a thermostable pectate lyase from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 58, 709-711.  
12221284 S.J.Charnock, I.E.Brown, J.P.Turkenburg, G.W.Black, and G.J.Davies (2002).
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
  Proc Natl Acad Sci U S A, 99, 12067-12072.
PDB codes: 1gxm 1gxn 1gxo
  10368144 C.Roy, H.Kester, J.Visser, V.Shevchik, N.Hugouvieux-Cotte-Pattat, J.Robert-Baudouy, and J.Benen (1999).
Modes of action of five different endopectate lyases from Erwinia chrysanthemi 3937.
  J Bacteriol, 181, 3705-3709.  
9100381 D.W.Bauer, and A.Collmer (1997).
Molecular cloning, characterization, and mutagenesis of a pel gene from Pseudomonas syringae pv. lachyrmans encoding a member of the Erwinia chrysanthemi pelADE family of pectate lyases.
  Mol Plant Microbe Interact, 10, 369-379.  
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.