PDBsum entry: 1r76

Lyase

PDB id: 1r76

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

Protein chain

Q9X592  (Q9X592_AZOIR) -  Pectate lyase

Seq: 432 a.a.

Struc: 384 a.a.

 Gene Ontology (GO) functional annotation 

• 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.