PDBsum entry 3ebb

Chaperone

PDB id: 3ebb

Contents

Protein chain

265 a.a. *

Ligands

LEU-TYR

ASP-LEU-TYR-GLY

LEU-TYR-GLY

ASP-LEU-TYR

Metals

_MG

Waters ×477

* Residue conservation analysis

PDB id:

3ebb

Name:

Chaperone

Title:

Plap/p97 complex

Structure:

Phospholipase a2-activating protein. Chain: a, b, c, d. Fragment: pul domain, residues 511-795. Synonym: plap, pla2p,doa1. Engineered: yes. Transitional endoplasmic reticulum atpase (ter atp. Chain: e, f, g, h. Fragment: c-terminal peptide, residues 797-806. Synonym: 15s mg(2+)-atpase p97 subunit, valosin-containing protein,

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: plaa, plap, flj11281, flj12699. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: occurs naturally in humans

Resolution:

1.90Å R-factor: 0.191 R-free: 0.248

Authors:

J.R.Walker,L.Qiu,M.Akutsu,Y.Slessarev,M.F.Amaya,Y.Li,C.Bountra, J.Weigelt,C.H.Arrowsmith,A.M.Edwards,A.Bochkarev,S.Dhe-Paganon, Structural Genomics Consortium (Sgc)

Key ref:

L.Qiu et al. (2010). Structure and function of the PLAA/Ufd3-p97/Cdc48 complex. J Biol Chem, 285, 365-372. PubMed id: 19887378 DOI: 10.1074/jbc.M109.044685

Date:

27-Aug-08 Release date: 24-Feb-09

Protein chains

Q9Y263  (PLAP_HUMAN) -  Phospholipase A-2-activating protein from Homo sapiens

Seq: 795 a.a.

Struc: 265 a.a.

DOI no: 10.1074/jbc.M109.044685

J Biol Chem 285:365-372 (2010)

PubMed id: 19887378

Structure and function of the PLAA/Ufd3-p97/Cdc48 complex.

L.Qiu, N.Pashkova, J.R.Walker, S.Winistorfer, A.Allali-Hassani, M.Akutsu, R.Piper, S.Dhe-Paganon.

ABSTRACT

PLAA (ortholog of yeast Doa1/Ufd3, also know as human PLAP or phospholipase A2-activating protein) has been implicated in a variety of disparate biological processes that involve the ubiquitin system. It is linked to the maintenance of ubiquitin levels, but the mechanism by which it accomplishes this is unclear. The C-terminal PUL (PLAP, Ufd3p, and Lub1p) domain of PLAA binds p97, an AAA ATPase, which among other functions helps transfer ubiquitinated proteins to the proteasome for degradation. In yeast, loss of Doa1 is suppressed by altering p97/Cdc48 function indicating that physical interaction between PLAA and p97 is functionally important. Although the overall regions of interaction between these proteins are known, the structural basis has been unavailable. We solved the high resolution crystal structure of the p97-PLAA complex showing that the PUL domain forms a 6-mer Armadillo-containing domain. Its N-terminal extension folds back onto the inner curvature forming a deep ridge that is positively charged with residues that are phylogenetically conserved. The C terminus of p97 binds in this ridge, where the side chain of p97-Tyr(805), implicated in phosphorylation-dependent regulation, is buried. Expressed in doa1Delta null cells, point mutants of the yeast ortholog Doa1 that disrupt this interaction display slightly reduced ubiquitin levels, but unlike doa1Delta null cells, showed only some of the growth phenotypes. These data suggest that the p97-PLAA interaction is important for a subset of PLAA-dependent biological processes and provides a framework to better understand the role of these complex molecules in the ubiquitin system.

Selected figure(s)

Figure 1.
Structure of the PUL domain. A, domain map of PLAA that defines N-terminal WD40 β-propeller (yellow), central PFU domain (blue), and C-terminal PUL domain (gray). Secondary structure elements are shown colored according to their ARM. B, overall structure of PUL domain containing six Armadillo repeats individually colored and labeled. All figures were generated with PyMol. C, stereoscopic view of the N-terminal extension in yellow stick format bound across the concave surface of the Armadillo fold, shown as light blue cylinders. The third helices of each Armadillo unit is labeled.

Figure 2.
Co-structure of the PUL domain with the C-terminal p97 peptide. A, electrostatic surface representation was generated with a gradient from −10 (red) to 10 (blue) kT/e of the PUL domain only. The bound p97 peptide is show in green stick format. B, surface representation of the PUL domain is shown in light gray with conserved residues in purple. C, stereoscopic view of the terminal p97 peptide residues LYG^806 bound to the PUL domain shown with helices in schematic format and labeled. PUL residues within proximity are shown in stick format and labeled. The hydrogen bond is shown as a black dashed line; water molecules are shown as red cross-hairs. D, schematic representation of p97 (black) interactions with PLAA (blue). E, three-dimensional alignment of the PLAA (green) and PNGase (cyan)-bound p97 peptides.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2010, 285, 365-372) copyright 2010.

Figures were selected by an automated process.