PDBsum entry: 2rkq

Immune system

PDB-id: 2rkq

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

169 a.a. *

Waters ×252

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2rkq

Name:

Immune system

Title:

Crystal structure of drosophila peptidoglycan recognition protein sd (pgrp-sd)

Structure:

Peptidoglycan-recognition protein-sd. Chain: a. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: pgrp-sd. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227. Expression_system_cell: schneider cells.

UniProt:

Q9VS97 (PGPSD_DROME)

Seq:

186 a.a.

Struc:

169 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Resolution:

1.50Å

R-factor:

0.156

R-free:

0.173

Authors:

A.Roussel,J.Royet,P.Leone,C.Kellenberger

Key ref:

P.Leone et al. (2008). Crystal structure of Drosophila PGRP-SD suggests binding to DAP-type but not lysine-type peptidoglycan.. Mol Immunol, 45, 2521-2530. [PubMed id: 18304640] [DOI: 10.1016/j.molimm.2008.01.015]

Date:

17-Oct-07

Release date:

25-Mar-08

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/j.molimm.2008.01.015

Mol Immunol 45:2521-2530 (2008)

PubMed id: 18304640

Crystal structure of Drosophila PGRP-SD suggests binding to DAP-type but not lysine-type peptidoglycan.

P.Leone, V.Bischoff, C.Kellenberger, C.Hetru, J.Royet, A.Roussel.

ABSTRACT

In Drosophila the synthesis of antimicrobial peptides in response to microbial infections is under the control of the Toll and immune deficiency (Imd) signaling pathways. The Toll signaling pathway responds mainly to Gram-positive bacterial and fungal infection while the Imd pathway mediates the response to Gram-negative bacteria. Microbial recognition upstream of Toll involves, at least in part, peptidoglycan recognition proteins (PGRPs). The sensing of Gram-positive bacteria is mediated by the pattern recognition receptors PGRP-SA and Gram-negative binding protein 1 (GNBP1) that cooperate to detect the presence of lysine-type peptidoglycan in the host. Recently it has been shown that a loss-of-function mutation in peptidoglycan recognition protein SD (PGRP-SD) severely exacerbates the PGRP-SA and GNBP1 mutant phenotypes. Here we have solved the crystal structure of PGRP-SD at 1.5A resolution. Comparison with available structures of PGRPs in complex with their peptidoglycan (PGN) ligand strongly suggests a diaminopimelic acid (DAP) specificity for PGRP-SD. This result is supported by pull-down assays with insoluble PGNs. In addition we show that Toll pathway activation after infection by DAP-type PGN containing bacteria is clearly reduced in PGRP-SD mutant flies. Our hypothesis is that the role of PGRP-SD is the recognition of DAP-type PGNs responsible for the activation of the Toll pathway by Gram-negative bacteria.