3NJV

Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex

Summary for 3NJV

• Entry DOI: 10.2210/pdb3njv/pdb
• Related: 1NKG 3NJX
• Descriptor: Rhamnogalacturonase B, alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-beta-D-galactopyranuronic acid, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: carbohydrate active enzyme, lyase, pectin degradation, polysaccharide lyase family 4
• Biological source: Aspergillus aculeatus
• Total number of polymer chains: 1
• Total formula weight: 55498.50

Authors

Jensen, M.H.,Otten, H.,Christensen, U.,Borchert, T.V.,Christensen, L.L.H.,Larsen, S.,Lo Leggio, L. (deposition date: 2010-06-18, release date: 2010-10-06, Last modification date: 2024-10-09)

Primary citation

Jensen, M.H.,Otten, H.,Christensen, U.,Borchert, T.V.,Christensen, L.L.,Larsen, S.,Leggio, L.L.
Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus aculeatus.
J.Mol.Biol., 404:100-111, 2010

PubMed Abstract: We present here the first experimental evidence for bound substrate in the active site of a rhamnogalacturonan lyase belonging to family 4 of polysaccharide lyases, Aspergillus aculeatus rhamnogalacturonan lyase (RGL4). RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide. Based on the previously determined wild-type structure, enzyme variants RGL4_H210A and RGL4_K150A have been produced and characterized both kinetically and structurally, showing that His210 and Lys150 are key active-site residues. Crystals of the RGL4_K150A variant soaked with a rhamnogalacturonan digest gave a clear picture of substrate bound in the -3/+3 subsites. The crystallographic and kinetic studies on RGL4, and structural and sequence comparison to other enzymes in the same and other PL families, enable us to propose a detailed reaction mechanism for the β-elimination on [-,2)-α-l-rhamno-(1,4)-α-d-galacturonic acid-(1,-]. The mechanism differs significantly from the one established for pectate lyases, in which most often calcium ions are engaged in catalysis.

PubMed: 20851126
DOI: 10.1016/j.jmb.2010.09.013

Experimental method

X-RAY DIFFRACTION (2.4 Å)