1R76

Structure of a pectate lyase from Azospirillum irakense

Summary for 1R76

• Entry DOI: 10.2210/pdb1r76/pdb
• Descriptor: pectate lyase, MERCURY (II) ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: a-helical structure, lyase
• Biological source: Azospirillum irakense
• Total number of polymer chains: 1
• Total formula weight: 45216.19

Authors

Novoa de Armas, H.,Verboven, C.,De Ranter, C.,Desair, J.,Vande Broek, A.,Vanderleyden, J.,Rabijns, A. (deposition date: 2003-10-20, release date: 2004-06-01, Last modification date: 2024-02-14)

Primary citation

Novoa De Armas, H.,Verboven, C.,De Ranter, C.,Desair, J.,Vande Broek, A.,Vanderleyden, J.,Rabijns, A.
Azospirillum irakense pectate lyase displays a toroidal fold.
Acta Crystallogr.,Sect.D, 60:999-1007, 2004

PubMed 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.

PubMed: 15159558
DOI: 10.1107/S090744490400602X

Experimental method

X-RAY DIFFRACTION (2.65 Å)