PDBsum entry: 1oht

Hydrolase

PDB id: 1oht

Contents

Protein chain

174 a.a. *

Ligands

EDO ×2

TLA

Metals

_ZN

Waters ×57

* Residue conservation analysis

PDB id:

1oht

Name:

Hydrolase

Title:

Peptidoglycan recognition protein-lb

Structure:

Cg14704 protein. Chain: a. Synonym: peptidoglycan recognition protein. Engineered: yes

Source:

Drosophila melanogaster. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.0Å R-factor: 0.216 R-free: 0.243

Authors:

M.-S.Kim,M.Byun,B.-H.Oh

Key ref:

M.S.Kim et al. (2003). Crystal structure of peptidoglycan recognition protein LB from Drosophila melanogaster. Nat Immunol, 4, 787-793. PubMed id: 12845326 DOI: 10.1038/ni952

Date:

31-May-03 Release date: 18-Jul-03

Protein chain

Q8INK6  (PGPLB_DROME) -  Peptidoglycan-recognition protein LB

Seq: 232 a.a.

Struc: 174 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.28 - N-acetylmuramoyl-L-alanine amidase.
• Reaction: Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: innate immune response (4 terms)
• Biochemical function: protein binding (6 terms)

DOI no: 10.1038/ni952

Nat Immunol 4:787-793 (2003)

PubMed id: 12845326

Crystal structure of peptidoglycan recognition protein LB from Drosophila melanogaster.

M.S.Kim, M.Byun, B.H.Oh.

ABSTRACT

The family of peptidoglycan recognition proteins (PGRPs) are associated with the recognition of the peptidoglycan of microbes and subsequent activation of signaling pathways for immune response. Here the crystal structure of Drosophila PGRP-LB is determined at a resolution of 2.0 A and shows an active-site cleft with a zinc cage. Poor conservation of surface residues at the cleft predicts a widely varying individual specificity of PGRPs for molecular patterns on microbial cell walls. At the back of this cleft is a putatively conserved distinctive groove. The location and mainly hydrophobic nature of the groove indicate that the back face serves for subsequent signaling after clustering of PGRP molecules by binding to polymeric cell wall components.

Selected figure(s)

Figure 2.
Figure 2. Structures of PGRP-LB and T7 lysozyme. (a) Left, ribbon diagram of PGRP-LB structure. The secondary structures are numbered in order of their appearance in the sequence. The isolated strand 2 adopts the typical backbone conformations of a -strand. Gold, the PGRP-specific segment at the N terminus, absent in T7 lysozyme. The single disulfide bond is shown as a 'ball-and-stick'. Right, T7 lysozyme structure (Protein Data Bank code, 1LBA). Bound zinc ions are shown as spheres. (b) Superposition of the C traces of the PGRP-LB (blue and gold) and T7 lysozyme structures (green). The C atoms of a set of residues in PGRP-LB (residues 36 -45, 60 -68, 71 -92, 94 -116, 122 -137 and 148 -162) and those in T7 lysozyme (residues 11 -20, 29 -37, 39 -60, 62 -84, 95 -110 and 118 -132) were superposed with an r.m.s. derivation value of 1.16 Å (for a total of 95 atoms). Gold lines indicate the PGRP-specific segments. The tubes in cyan indicate the C 'worms' of residues 178 -184 of a symmetry mate occupying the active-site cleft of PGRP-LB. Every 20th residue of PGRP-LB and lysozyme is indicated as a numbered knob. The orientation of the molecules is the same as in a.

Figure 3.
Figure 3. The PGRP-specific segment constituted a distinctive back face. (a) 'Stereo view' of representative interactions of the PGRP-specific segment with other parts of PGRP-LB. Regions around Arg18 and Trp21 are shown along with the final 2F[o]-F[c] map (2.0 Å, 1.1 ). Dotted lines indicate the hydrogen and ionic bonds. (b) Comparison of the back faces of PGRP-LB (left) and T7 lysozyme (right). The PGRP-specific segment (in orange) is absent from T7 lysozyme. The segment adopts mainly extended -strand and loop structures. (c) Electrostatic surface representation (red, negative; blue, positive) of the back faces of PGRP-LB and T7 lysozyme. The orientation of the molecules is the same as in b and is shown as a view down the groove between 1 and 2. Gold letters and numbers, surface-exposed residues that are greater than 80% conserved.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Immunol (2003, 4, 787-793) copyright 2003.

Figures were selected by an automated process.