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9k1n

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Crystal structure of family 11 xylanase in complex with inhibitor (OsXIP)

Structural highlights

9k1n is a 4 chain structure with sequence from Oryza sativa Japonica Group and Rhizopus arrhizus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.205Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYN2_RHIOR

Publication Abstract from PubMed

Plants have evolved xylanase inhibitor proteins as part of their defense mechanisms against phytopathogens. The rice xylanase inhibitor protein (OsXIP) is structurally similar to GH18 chitinase and homologous to wheat XIP-type inhibitor (XIP-I), which inhibits both GH10 and GH11 xylanases. Various inhibition and interaction analyses showed that OsXIP competitively inhibits the hydrolytic activity of GH11 xylanase RXyn2, but not the activity of GH10 xylanase RXyn1 from Rhizopus oryzae. The crystal structure of the OsXIP/RXyn2 complex showed that OsXIP, which has a (beta/alpha)(8)-barrel fold, extrudes the loop between alpha4 and beta5 (Lalpha4beta5(OsXIP)) and inserts the loop into the xylotriose binding site (-3 to -1 subsite) formed by the inner beta-sheet (palm) of RXyn2 jelly roll. The guanidyl group of Arg155 in Lalpha4beta5(OsXIP) was shown to be critical for the inhibitory activity by mutational analysis. Notably, in the complex structure, the cylindrical cavity formed by the palm of RXyn2 jelly roll stacked upright on the loops at the N terminal ends of the beta-strands of OsXIP (I-formation). On the other hand, in the complex structure of XIP-I and GH11 xylanase from Talaromyces funiculosus (XYNC), the cavity of XYNC laid tangentially to the part of the corresponding region of XIP-I through the Lalpha4beta5(XIP-I) (T-formation). The dissociation constant of the OsXIP/RXyn2 complex was one-tenth of that of the XIP-I/XYNC complex (4.2 versus 41.5 nM). OsXIP may have adapted to bind and inhibit GH11 enzymes, which are resistant to the inhibition by XIP-I type proteins, by changing its binding mode.

Molecular arrangements that accompany binding of rice xylanase inhibitor protein OsXIP and the Rhizopus oryzae GH11 xylanase RXyn2.,Ohnuma T, Tanaka J, Ozaki H, Mitsui K, Tsujitsugu D, Okugawa M, Takeda T, Ihara M, Fukamizo T, Takeshita D J Biol Chem. 2025 Aug;301(8):110385. doi: 10.1016/j.jbc.2025.110385. Epub 2025 , Jun 16. PMID:40533062^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ohnuma T, Tanaka J, Ozaki H, Mitsui K, Tsujitsugu D, Okugawa M, Takeda T, Ihara M, Fukamizo T, Takeshita D. Molecular arrangements that accompany binding of rice xylanase inhibitor protein OsXIP and the Rhizopus oryzae GH11 xylanase RXyn2. J Biol Chem. 2025 Aug;301(8):110385. PMID:40533062 doi:10.1016/j.jbc.2025.110385