PDBsum entry: 1sxr

Immune system

PDB id: 1sxr

Contents

Protein chains

173 a.a. *

Ligands

SO4 ×2

EDO ×4

Waters ×388

* Residue conservation analysis

PDB id:

1sxr

Name:

Immune system

Title:

Drosophila peptidoglycan recognition protein (pgrp)-sa

Structure:

Peptidoglycan recognition protein sa cg11709-pa. Chain: a, b. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227. Expression_system_cell: sc2.

Resolution:

1.56Å R-factor: 0.181 R-free: 0.211

Authors:

J.B.Reiser,L.Teyton,I.A.Wilson

Key ref:

J.B.Reiser et al. (2004). Crystal structure of the Drosophila peptidoglycan recognition protein (PGRP)-SA at 1.56 A resolution. J Mol Biol, 340, 909-917. PubMed id: 15223330 DOI: 10.1016/j.jmb.2004.04.077

Date:

31-Mar-04 Release date: 29-Jun-04

Protein chains

Q9VYX7  (PGPSA_DROME) -  Peptidoglycan-recognition protein SA

Seq: 203 a.a.

Struc: 173 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.17.13 - Muramoyltetrapeptide carboxypeptidase.
• Reaction: GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H₂O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine

GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H(2)O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine (Bound ligand (Het Group name = EDO) matches with 42.86% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: immune response (10 terms)
• Biochemical function: protein binding (9 terms)

Key reference

DOI no: 10.1016/j.jmb.2004.04.077

J Mol Biol 340:909-917 (2004)

PubMed id: 15223330

Crystal structure of the Drosophila peptidoglycan recognition protein (PGRP)-SA at 1.56 A resolution.

J.B.Reiser, L.Teyton, I.A.Wilson.

ABSTRACT

Peptidoglycan recognition proteins (PGRPs) form a recently discovered protein family, which is conserved from insect to mammals and is implicated in the innate immune system by interacting with/or degrading microbial peptidoglycans (PGNs). Drosophila PGRP-SA is a member of this family of pattern recognition receptors and is involved in insect Toll activation. We report here the crystal structure of PGRP-SA at 1.56 A resolution, which represents the first example of a "recognition" PGRP. Comparison with the catalytic Drosophila PGRP-LB reveals an overall structure conservation with an L-shaped hydrophilic groove that is likely the PGN carbohydrate core binding site, but further suggests some possible functional homology between recognition and catalytic PGRPs. Consistent with sequence analysis, PGRP-SA does not contain the canonical zinc-binding residues found in catalytic PGRPs. However, substitution of the zinc-binding cysteine residue by serine, along with an altered coordinating histidine residue, assembles a constellation of residues that resembles a modified catalytic triad. The serine/histidine juxtaposition to a threonine residue and a carbonyl oxygen atom, along with conservation of the catalytic water molecule found in PGRP-LB, tantalizingly suggests some hydrolytic function for this member of receptor PGRPs.

Selected figure(s)

Figure 1.
Figure 1. Stereoview of PGRP-SA crystal structure. The ribbon structure of PGRP-SA from D. melagonaster is represented and the secondary structures are labeled in order from N to C terminus. The disulfide bonds between Cys11 and Cys134, and between Cys48 and Cys54 are drawn in yellow ball-and-sticks. The six-histidine tag at the C terminus is shown in white.

Figure 6.
Figure 6. PGRP-SA Ser/His juxtaposition in comparison with the catalytic center of PGRP-LB and serine hydrolases. (a) Histidine 41, serine 158, threonine 99 and the carbonyl group of residue 98 of PGRP-SA are represented in ball and sticks. Atoms are colored according to their type. Hydrogen bonds are represented in broken lines and distances in Å. (b) Although structural changes are observed compared to PGRP-LB, the location of the presumed catalytic water molecule OS is structurally conserved. (c) The Ser/His/Asp triad of bovine trypsin (PDB access code: 1TRN) and (d) the modified triad of a bacterial esterase (PDB access code: 1ESC) are shown for comparison. The configuration of PGRP-SA S158/H41/T99/H98-carbonyl resembles the catalytic center of serine hydrolases, especially the modified triad of bacterial esterase.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 340, 909-917) copyright 2004.

Figures were selected by an automated process.