PDBsum entry 1xdf

Plant protein

PDB id: 1xdf

Contents

Protein chains

157 a.a. *

Ligands

EPE

Metals

_NA

Waters ×281

* Residue conservation analysis

PDB id:

1xdf

Name:

Plant protein

Title:

Crystal structure of pathogenesis-related protein llpr-10.2a from yellow lupine

Structure:

Pr10.2a. Chain: a, b. Synonym: llpr-10.2a. Engineered: yes

Source:

Lupinus luteus. Yellow lupine. Organism_taxid: 3873. Gene: llpr-10.2a. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.90Å R-factor: 0.207 R-free: 0.251

Authors:

O.Pasternak,J.Biesiadka,R.Dolot,L.Handschuh,G.Bujacz,M.M.Sikorski, M.Jaskolski

Key ref:

O.Pasternak et al. (2005). Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass. Acta Crystallogr D Biol Crystallogr, 61, 99. PubMed id: 15608381 DOI: 10.1107/S0907444904028173

Date:

06-Sep-04 Release date: 15-Feb-05

Protein chains

Q9LLQ3  (P102A_LUPLU) -  Class 10 plant pathogenesis-related protein 2A from Lupinus luteus

Seq: 158 a.a.

Struc: 157 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.27.- - ?????

DOI no: 10.1107/S0907444904028173

Acta Crystallogr D Biol Crystallogr 61:99 (2005)

PubMed id: 15608381

Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass.

O.Pasternak, J.Biesiadka, R.Dolot, L.Handschuh, G.Bujacz, M.M.Sikorski, M.Jaskolski.

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.

Selected figure(s)

Figure 3.
Figure 3 A stereoview illustrating the conformation of helix 3 (shown without side chains, except Lys136 and Arg138) in LlPR-10.2A (molecule A). A kink of almost 60° in the middle of the helix is well supported by the 2F[o] - F[c] electron-density map (contoured at the 1.0 level). The helix is stabilized by salt bridges formed by Lys136 and Arg138 and by hydrophobic interactions with the -sheet (not shown).

Figure 6.
Figure 6 Superposition of all PR-10 molecules of known X-ray structure. The position of Tyr149 (Tyr148 in LlPR-10.1 and Tyr150 in Bet v 1) is indicated to show the axial shift of helix 3 in Bet v 1. Calculations were performed in ALIGN (Cohen, 1997[Cohen, G. R. (1997). J. Appl. Cryst. 30, 1160-1161.]) using C^ -atom positions.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 99-0) copyright 2005.

Figures were selected by the author.