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PDBsum entry 1r76

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protein ligands metals links
Lyase PDB id
1r76
Jmol
Contents
Protein chain
384 a.a. *
Ligands
IPA
GOL ×4
Metals
_HG
_CL
Waters ×254
* Residue conservation analysis
PDB id:
1r76
Name: Lyase
Title: Structure of a pectate lyase from azospirillum irakense
Structure: Pectate lyase. Chain: a. Fragment: residues 25-432. Engineered: yes
Source: Azospirillum irakense. Organism_taxid: 34011. Gene: pela. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.65Å     R-factor:   0.198     R-free:   0.262
Authors: H.Novoa De Armas,C.Verboven,C.De Ranter,J.Desair,A.Vande Bro J.Vanderleyden,A.Rabijns
Key ref:
H.Novoa De Armas et al. (2004). Azospirillum irakense pectate lyase displays a toroidal fold. Acta Crystallogr D Biol Crystallogr, 60, 999. PubMed id: 15159558 DOI: 10.1107/S090744490400602X
Date:
20-Oct-03     Release date:   01-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X592  (Q9X592_AZOIR) -  Pectate lyase
Seq:
Struc:
432 a.a.
384 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     lyase activity     1 term  

 

 
DOI no: 10.1107/S090744490400602X Acta Crystallogr D Biol Crystallogr 60:999 (2004)
PubMed id: 15159558  
 
 
Azospirillum irakense pectate lyase displays a toroidal fold.
H.Novoa De Armas, C.Verboven, C.De Ranter, J.Desair, A.Vande Broek, J.Vanderleyden, A.Rabijns.
 
  ABSTRACT  
 
The three-dimensional structure of Azospirillum irakense pectate lyase (PelA) has been determined at a resolution of 2.65 A. The crystals are hexagonal, belonging to space group P6(5)22, with unit-cell parameters a = b = 85.37, c = 231.32 angstroms. Phase information was derived from a multiple-wavelength anomalous dispersion (MAD) experiment using a Hg derivative. Refinement of the model converged to Rcryst = 20.08% and Rfree = 25.87%. The overall structure of PelA does not adopt the characteristic parallel beta-helix fold displayed by pectate lyases from polysaccharide lyase (PL) families PL1, PL3 and PL9. Instead, it displays a predominantly alpha-helical structure with irregular coils and short beta-strands, similar to the recently reported structure of the catalytic module of the Cellvibrio japonicus pectate lyase Pel10Acm. The topologies of the two structures have been compared. They show two 'domains' with the interface between them being a wide-open central groove in which the active site is located. The active sites of the crystal structures are also compared and their similarities and differences are discussed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Generic catalytic mechanism ( -elimination mechanism) for a polysaccharide lyase. The generally accepted mechanism involves proton abstraction from C5 of the +1 subsite sugar residue adjacent to the C6 carboxyl moiety to release the 4,5-unsaturated product via a -elimination mechanism (Henrissat et al., 2001[Henrissat, B., Coutinho, P. M. & Davies, G. J. (2001). Plant Mol. Biol. 47, 55-72.]). R', monosaccharide unit, R[1], alkyl or H.
Figure 5.
Figure 5 Putative reaction mechanism for PL10 enzymes, as proposed by Charnock et al. (2002[Charnock, S. J., Brown, I. E., Turkenburg, J. P., Black, G. W. & Davies, G. J. (2002). Proc. Natl Acad. Sci. USA, 99, 12067-12072.]). Proton abstraction by arginine is followed by leaving-group elimination.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 999-0) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
17881361 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.
PDB codes: 2v8i 2v8j 2v8k
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.