4QAW

Structure of modular Xyn30D from Paenibacillus barcinonensis

Summary for 4QAW

• Entry DOI: 10.2210/pdb4qaw/pdb
• Related: 4QB1 4QB2 4QB6
• Descriptor: Xyn30D, CALCIUM ION (3 entities in total)
• Functional Keywords: tim barrel, beta-structure, hydrolase, carbohydrate/sugar binding, calcium binding, tim barrel beta-structure, carbohydrate/sugar binding calcium binding, plant-cell wall degradation
• Biological source: Paenibacillus barcinonensis
• Total number of polymer chains: 8
• Total formula weight: 498118.78

Authors

Sainz-Polo, M.A.,Sanz-Aparicio, J. (deposition date: 2014-05-06, release date: 2014-10-08, Last modification date: 2023-09-20)

Primary citation

Sainz-Polo, M.A.,Valenzuela, S.V.,Gonzalez, B.,Pastor, F.I.,Sanz-Aparicio, J.
Structural Analysis of Glucuronoxylan-specific Xyn30D and Its Attached CBM35 Domain Gives Insights into the Role of Modularity in Specificity.
J.Biol.Chem., 289:31088-31101, 2014

PubMed Abstract: Glucuronoxylanase Xyn30D is a modular enzyme containing a family 30 glycoside hydrolase catalytic domain and an attached carbohydrate binding module of the CBM35 family. We present here the three-dimensional structure of the full-length Xyn30D at 2.4 Å resolution. The catalytic domain folds into an (α/β)8 barrel with an associated β-structure, whereas the attached CBM35 displays a jellyroll β-sandwich including two calcium ions. Although both domains fold in an independent manner, the linker region makes polar interactions with the catalytic domain, allowing a moderate flexibility. The ancillary Xyn30D-CBM35 domain has been expressed and crystallized, and its binding abilities have been investigated by soaking experiments. Only glucuronic acid-containing ligands produced complexes, and their structures have been solved. A calcium-dependent glucuronic acid binding site shows distinctive structural features as compared with other uronic acid-specific CBM35s, because the presence of two aromatic residues delineates a wider pocket. The nonconserved Glu(129) makes a bidentate link to calcium and defines region E, previously identified as specificity hot spot. The molecular surface of Xyn30D-CBM35 shows a unique stretch of negative charge distribution extending from its binding pocket that might indicate some oriented interaction with its target substrate. The binding ability of Xyn30D-CBM35 to different xylans was analyzed by affinity gel electrophoresis. Some binding was observed with rye glucuronoarabinoxylan in presence of calcium chelating EDTA, which would indicate that Xyn30D-CBM35 might establish interaction to other components of xylan, such as arabinose decorations of glucuronoarabinoxylan. A role in depolymerization of highly substituted chemically complex xylans is proposed.

PubMed: 25202007
DOI: 10.1074/jbc.M114.597732

Experimental method

X-RAY DIFFRACTION (2.4 Å)