4PMZ

Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylobiose

Summary for 4PMZ

• Entry DOI: 10.2210/pdb4pmz/pdb
• Related: 4PMX 4PMY
• Related PRD ID: PRD_900116
• Descriptor: Xylanase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: xylanase, hydrolase
• Biological source: Xanthomonas axonopodis pv. citri
• Total number of polymer chains: 2
• Total formula weight: 69043.28

Authors

Santos, C.R.,Martins, V.P.M.,Zanphorlin, L.M.,Ruller, R.,Murakami, M.T. (deposition date: 2014-05-22, release date: 2014-10-08, Last modification date: 2023-09-27)

Primary citation

Santos, C.R.,Hoffmam, Z.B.,de Matos Martins, V.P.,Zanphorlin, L.M.,de Paula Assis, L.H.,Honorato, R.V.,Lopes de Oliveira, P.S.,Ruller, R.,Murakami, M.T.
Molecular mechanisms associated with xylan degradation by xanthomonas plant pathogens.
J.Biol.Chem., 289:32186-32200, 2014

PubMed Abstract: Xanthomonas pathogens attack a variety of economically relevant plants, and their xylan CUT system (carbohydrate utilization with TonB-dependent outer membrane transporter system) contains two major xylanase-related genes, xynA and xynB, which influence biofilm formation and virulence by molecular mechanisms that are still elusive. Herein, we demonstrated that XynA is a rare reducing end xylose-releasing exo-oligoxylanase and not an endo-β-1,4-xylanase as predicted. Structural analysis revealed that an insertion in the β7-α7 loop induces dimerization and promotes a physical barrier at the +2 subsite conferring this unique mode of action within the GH10 family. A single mutation that impaired dimerization became XynA active against xylan, and high endolytic activity was achieved when this loop was tailored to match a canonical sequence of endo-β-1,4-xylanases, supporting our mechanistic model. On the other hand, the divergent XynB proved to be a classical endo-β-1,4-xylanase, despite the low sequence similarity to characterized GH10 xylanases. Interestingly, this enzyme contains a calcium ion bound nearby to the glycone-binding region, which is required for catalytic activity and structural stability. These results shed light on the molecular basis for xylan degradation by Xanthomonas and suggest how these enzymes synergistically assist infection and pathogenesis. Our findings indicate that XynB contributes to breach the plant cell wall barrier, providing nutrients and facilitating the translocation of effector molecules, whereas the exo-oligoxylanase XynA possibly participates in the suppression of oligosaccharide-induced immune responses.

PubMed: 25266726
DOI: 10.1074/jbc.M114.605105

Experimental method

X-RAY DIFFRACTION (1.401 Å)