1XDF

Crystal structure of pathogenesis-related protein LlPR-10.2A from yellow lupine

Summary for 1XDF

• Entry DOI: 10.2210/pdb1xdf/pdb
• Related: 1BV1 1FM4 1ICX 1IFV
• Descriptor: PR10.2A, SODIUM ION, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: 7-stranded antiparallel beta-sheet, kinked c-terminal alpha-helix, glycine-rich loop, plant protein
• Biological source: Lupinus luteus (yellow lupine)
• Total number of polymer chains: 2
• Total formula weight: 33846.94

Authors

Pasternak, O.,Biesiadka, J.,Dolot, R.,Handschuh, L.,Bujacz, G.,Sikorski, M.M.,Jaskolski, M. (deposition date: 2004-09-06, release date: 2005-02-15, Last modification date: 2023-10-25)

Primary citation

Pasternak, O.,Biesiadka, J.,Dolot, R.,Handschuh, L.,Bujacz, G.,Sikorski, M.M.,Jaskolski, M.
Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass.
Acta Crystallogr.,Sect.D, 61:99-107, 2005

PubMed Abstract: Pathogenesis-related (PR) proteins of class 10 are abundant in higher plants. Some of these proteins are induced under stress conditions as part of the plant defence mechanism. Other homologues are developmentally regulated and their expression varies in different plant organs. The PR-10 proteins are encoded by multigene families, have a weight of about 17 kDa and are found in the cytosol. In yellow lupin, nine different homologues have been identified and divided into two subclasses, LlPR-10.1 and LlPR-10.2. Within each subclass the sequence identity is about 75-91%, while across the subclasses it is only 59-60%. Here, the crystal structure of a yellow lupin PR-10 protein from the second subclass, LlPR-10.2A, is presented. The structure was solved by molecular replacement and refined to R = 0.205 using 1.9 A resolution data. The general fold of LlPR-10.2A resembles that of the other PR-10 proteins and consists of a long C-terminal alpha-helix surrounded by a seven-stranded antiparallel beta-sheet, with two shorter alpha-helices located between strands beta1 and beta2. The most variable part of the structure, the C-terminal helix, is strongly kinked towards the beta-sheet core in both LlPR-10.2A molecules present in the asymmetric unit. This unexpected feature reduces the size of the hydrophobic cavity observed in other PR-10 proteins that is reported to be the ligand-binding site. As in other PR-10 structures, a surface loop located near the entrance to the cavity shows very high structural conservation and stability despite the high glycine content in its sequence.

PubMed: 15608381
DOI: 10.1107/S0907444904028173

Experimental method

X-RAY DIFFRACTION (1.9 Å)