PDBsum entry 1r4n

Cell cycle

PDB id: 1r4n

Contents

Protein chains

516 a.a. *

418 a.a. *

76 a.a. *

Ligands

ATP ×4

Metals

_ZN ×4

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The structure of the appbp1-Uba3-Nedd8-Atp complex reveals the basis for selective ubiquitin-Like protein activation by an e1.

Authors

H.Walden, M.S.Podgorski, D.T.Huang, D.W.Miller, R.J.Howard, D.L.Minor, J.M.Holton, B.A.Schulman.

Ref.

Mol Cell, 2003, 12, 1427-1437. [DOI no: 10.1016/S1097-2765(03)00452-0]

PubMed id

14690597

Abstract

E1 enzymes initiate ubiquitin-like protein (ubl) transfer cascades by catalyzing adenylation of the ubl's C terminus. An E1's selectivity for its cognate ubl is essential because the E1 subsequently coordinates the ubl with its correct downstream pathway. We report here the structure of the 120 kDa quaternary complex between human APPBP1-UBA3, a heterodimeric E1, its ubl NEDD8, and ATP. The E1 selectively recruits NEDD8 through a bipartite interface, involving a domain common to all ubl activating enzymes including bacterial ancestors, and also eukaryotic E1-specific sequences. By modeling ubiquitin into the NEDD8 binding site and performing mutational analysis, we identify a single conserved arginine in APPBP1-UBA3 that acts as a selectivity gate, preventing misactivation of ubiquitin by NEDD8's E1. NEDD8 residues that interact with E1 correspond to residues in ubiquitin important for binding the proteasome and other ubiquitin-interacting proteins, suggesting that the conjugation and recognition machineries have coevolved for each specific ubl.

Figure 1.
Figure 1. Stereo Views of Electron Density Maps(A) NEDD8 displayed in the initial NCS-averaged 2Fo-Fc map contoured at 1.5σ, calculated from the original model lacking NEDD8.(B) Detail from the final refined 2Fo-Fc map showing NEDD8 interaction with UBA3 contoured at 1.5σ.

Figure 2.
Figure 2. Overall Structure of the APPBP1-UBA3-NEDD8-ATP ComplexThree views of the complex are shown in cartoon (top) and space-filling representations (bottom), each view a 35°–55° rotation around the y axis as indicated. APPBP1 is shown in blue, UBA3 in red, NEDD8 in yellow, and the position of the catalytic cysteine (C216A here) in green. The location of ATP is indicated in each view in the cartoon representations. The adenylation domain, the catalytic cysteine domain, and the C-terminal domain (CTD) are indicated. Figures were made using Pymol (DeLano, 2002).

The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 12, 1427-1437) copyright 2003.