PDBsum entry 1p9h

Cell adhesion

PDB id: 1p9h

Contents

Protein chain

179 a.a. *

Waters ×105

* Residue conservation analysis

PDB id:

1p9h

Name:

Cell adhesion

Title:

Crystal structure of the collagen-binding domain of yersinia adhesin yada

Structure:

Invasin. Chain: a. Fragment: collagen-binding domain. Synonym: outer membrane adhesin. Engineered: yes

Source:

Yersinia enterocolitica. Organism_taxid: 630. Gene: yada or yopa or inva or yop1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PDB file)

Resolution:

1.55Å R-factor: 0.196 R-free: 0.204

Authors:

H.Nummelin,M.C.Merckel,M.Skurnik,A.Goldman

Key ref:

H.Nummelin et al. (2004). The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll. EMBO J, 23, 701-711. PubMed id: 14765110 DOI: 10.1038/sj.emboj.7600100

Date:

12-May-03 Release date: 23-Mar-04

Protein chain

P31489  (YADA1_YEREN) -  Adhesin YadA from Yersinia enterocolitica

Seq: 455 a.a.

Struc: 179 a.a.

DOI no: 10.1038/sj.emboj.7600100

EMBO J 23:701-711 (2004)

PubMed id: 14765110

The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll.

H.Nummelin, M.C.Merckel, J.C.Leo, H.Lankinen, M.Skurnik, A.Goldman.

ABSTRACT

The crystal structure of the recombinant collagen-binding domain of Yersinia adhesin YadA from Yersinia enterocolitica serotype O:3 was solved at 1.55 A resolution. The trimeric structure is composed of head and neck regions, and the collagen binding head region is a novel nine-coiled left-handed parallel beta-roll. Before the beta-roll, the polypeptide loops from one monomer to the rest, and after the beta-roll the neck region does the same, making the transition from the globular head region to the narrower stalk domain. This creates an intrinsically stable 'lock nut' structure. The trimeric form of YadA is required for collagen binding, and mutagenesis of its surface residues allowed identification of a putative collagen-binding surface. Furthermore, a new structure-sequence motif for YadA beta-roll was used to identify putative YadA-head-like domains in a variety of human and plant pathogens. Such domains may therefore be a common bacterial strategy for avoiding host response.

Selected figure(s)

Figure 4.
Figure 4 (A) Organisation of the neck region in the C-terminus of the head domain, viewed from the C-terminus along the z-axis. The safety-pin structures as well as the beginnings of the stalk domain helices are shown. Some residues in the neck region are numbered for the magenta monomer for clarity. (B) The neck region (viewed perpendicular to (A) showing one multi-centre ionic network in the safety-pin region. It ties the three 'safety pins' to the central -roll assembly. The colouring of the monomers is the same as in Figure 1C.

Figure 5.
Figure 5 Most likely orientation of the collagen triple helix on the surface of the trimeric YadA head domain. The mutant residues are coloured according to their effect on type I collagen so that the mutants that abolished the binding totally are coloured red, to <20% in orange and the ones that attenuated the binding in violet. The residues D180 and E182, which also had an effect on the trimeric structure, are in blue. The figure was prepared using PyMOL (DeLano, 2002).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 701-711) copyright 2004.

Figures were selected by an automated process.