PDBsum entry: 1xu0

Membrane protein

PDB id: 1xu0

Contents

Protein chain

102 a.a. *

* Residue conservation analysis

PDB id:

1xu0

Name:

Membrane protein

Title:

Solution structure of xenopus leavis prion protein

Structure:

Prion protein. Chain: a. Fragment: globular domain(residues 98-226). Synonym: xlprp. Engineered: yes

Source:

Xenopus laevis. African clawed frog. Organism_taxid: 8355. Gene: prnp. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

20 models

Authors:

D.R.Perez,K.Wuthrich

Key ref:

L.Calzolai et al. (2005). Prion protein NMR structures of chickens, turtles, and frogs. Proc Natl Acad Sci U S A, 102, 651-655. PubMed id: 15647366 DOI: 10.1073/pnas.0408939102

Date:

25-Oct-04 Release date: 04-Jan-05

Protein chain

Q5S1W7  (Q5S1W7_XENLA) -  Major prion protein (Fragment)

Seq: 171 a.a.

Struc: 102 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)
• Biological process: protein homooligomerization (1 term)

DOI no: 10.1073/pnas.0408939102

Proc Natl Acad Sci U S A 102:651-655 (2005)

PubMed id: 15647366

Prion protein NMR structures of chickens, turtles, and frogs.

L.Calzolai, D.A.Lysek, D.R.Pérez, P.Güntert, K.Wüthrich.

ABSTRACT

The NMR structures of the recombinant prion proteins from chicken (Gallus gallus; chPrP), the red-eared slider turtle (Trachemys scripta; tPrP), and the African clawed frog (Xenopus laevis; xlPrP) are presented. The amino acid sequences of these prion proteins show approximately 30% identity with mammalian prion proteins. All three species form the same molecular architecture as mammalian PrPC, with a long, flexibly disordered tail attached to the N-terminal end of a globular domain. The globular domain in chPrP and tPrP contains three alpha-helices, one short 3(10)-helix, and a short antiparallel beta-sheet. In xlPrP, the globular domain includes three alpha-helices and a somewhat longer beta-sheet than in the other species. The spatial arrangement of these regular secondary structures coincides closely with that of the globular domain in mammalian prion proteins. Based on the low sequence identity to mammalian PrPs, comparison of chPrP, tPrP, and xlPrP with mammalian PrPC structures is used to identify a set of essential amino acid positions for the preservation of the same PrPC fold in birds, reptiles, amphibians, and mammals. There are additional conserved residues without apparent structural roles, which are of interest for the ongoing search for physiological functions of PrPC in healthy organisms.

Selected figure(s)

Figure 1.
Fig. 1. Sequence alignment of hPrP, chPrP, tPrP, and xlPrP, where hPrP represents "mammalian-type PrP." At the top is the residue numbering for hPrP, which is used throughout this manuscript, i.e., insertions and deletions in chPrP, tPrP, and xlPrP required for maximal coincidence with hPrP are not consecutively numbered. In this alignment, the amino acids shown in red are identical in all four PrPs, and the ones displayed in blue are identical in chPrP, tPrP, and hPrP. The black box identifies the segment containing polypeptide repeats (see text) for which no individual alignments were attempted. The GPI attachment site is identified with a green box, and the glycosylation sites (asparagine attachment site and nearest-next threonine/serine) is identified with light blue boxes. The orange boxes indicate segments with higher than average sequence conservation that do not have an apparent stabilizing role in the PrP fold, and might thus be conserved for functional reasons. These include the polypeptide segment 23-42 with the N-terminal signaling-peptide cleavage site, which has been suggested to be the signaling-peptide for reinternalization of PrP (36), a Src homology 3 (SH3)-binding motif of residues 100-110 (37, 38), the segment 113-128 representing a predicted transmembrane helix (39, 40), and the segment 146-155 in hPrP, chPrP, and tPrP that shows similarity to the laminin 2-chain (see text). The pink boxes indicate segments with high amino acid identity that appear to be needed for the stability of the "PrP-fold" (see text). At the bottom, the regular secondary structures in the globular domain of the four proteins are indicated. The sequence alignment was performed interactively so as to align a maximal number of identical residues. For the globular domain (121-230), the alignment was also based on visual inspection of the three-dimensional structures. In chPrP, the insertion at the end of helix 2 was divided into two segments to properly align the glycosylation site 197-199.

Figure 2.
Fig. 2. NMR structures of the globular domains of hPrP, chPrP, tPrP, and xlPrP. The polypeptide backbone fold for the residues 126-230 (see Fig. 1 for the sequence numbering used) and the core side chains with <20% solvent accessibility are shown for each species, as a superposition of the 20 conformers used to represent the NMR structure. The following side chains are included (see Fig. 1 for the sequence information): 141, 149 (only for chPrP and xlPrP), 150 (only for hPrP and xlPrP), 161, 162, 164 (only for xlPrP), 175, 176, 179, 180 (only for hPrP, chPrP, and tPrP), 183, 184, 205, 206, 209, 210, 213, 214, and 218. (A) hPrP (side chains shown in pink). (B) chPrP (side chains shown in blue). (C) tPrP (side chains shown in green). (D) xlPrP (side chains shown in yellow).

Figures were selected by an automated process.