PDBsum entry 1d2n

Hexamerization domain

PDB id

1d2n

Contents

			Protein chain

					246 a.a. *

			Ligands

					ANP


					GOL

			Metals

					_MG

			Waters ×271

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the hexamerization domain of n-Ethylmaleimide-Sensitive fusion protein.

Authors

C.U.Lenzen, D.Steinmann, S.W.Whiteheart, W.I.Weis.

Ref.

Cell, 1998, 94, 525-536. [DOI no: 10.1016/S0092-8674(00)81593-7]

PubMed id

9727495

Abstract

N-ethylmaleimide-sensitive fusion protein (NSF) is a cytosolic ATPase required for many intracellular vesicle fusion reactions. NSF consists of an amino-terminal region that interacts with other components of the vesicle trafficking machinery, followed by two homologous ATP-binding cassettes, designated D1 and D2, that possess essential ATPase and hexamerization activities, respectively. The crystal structure of D2 bound to Mg2+-AMPPNP has been determined at 1.75 A resolution. The structure consists of a nucleotide-binding and a helical domain, and it is unexpectedly similar to the first two domains of the clamp-loading subunit delta' of E. coli DNA polymerase III. The structure suggests several regions responsible for coupling of ATP hydrolysis to structural changes in full-length NSF.



	Figure 1. Figure 1. Structure of the NSF D2 Protomer(A) Topology of D2. Helices are shown as cylinders; strands are shown as as arrows. Residue numbers at the beginning and end of the principal elements of secondary structure are indicated, as well as the locations of the P loop and the DExx box (DDIE in D2). Helices and strands are numbered consecutively in sequence.(B) Stereo C[α] trace of D2. Every tenth C[α] is shown as a small sphere and numbered. The bound AMPPNP is shown with thickened black bonds.(C) Ribbon diagram of D2, with AMPPNP shown in a ball-and-stick representation. To aid in following the path of the backbone, the ribbon is white at the N terminus and becomes progressively darker moving toward the C terminus. The P loop and DExx box are green and red, respectively.(D) Ribbon diagram of the first two domains of E. coli DNA polymerase III δ′ ([22]), shown in the same orientation and color scheme as (C), except for a zinc-binding insert unique to δ′ (α3), which is shown in white. (B)–(D), as well as Figure 2B and Figure 3, were prepared with MOLSCRIPT ( [28]).		Figure 2. Figure 2. Nucleotide Binding by D2(A) Stereo view of the refined 2F[o]−F[c] electron density map within 2.4 Å of AMPPNP, contoured at 1.5 σ. The refined model is shown with AMPPNP and Mg^2PLUSPUSSIGN in black, and protein and water molecules in white. The figure was prepared with BOBSCRIPT ([18]).(B) Stereo view of nucleotide-binding site. AMPPNP is shown with black bonds. White, light gray, dark gray, and black spheres denote carbon, nitrogen, oxygen, and phosphorus atoms, respectively. Mg^2PLUSPUSSIGN is shown as a larger black sphere. Water molecules are shown as single oxygen atoms. Hydrogen bonds are shown as thin dashed lines; Mg^2PLUSPUSSIGN coordination bonds are shown as thick dashed lines. For clarity, the backbone at position 510 and the water molecule that interacts with the α-phosphate oxygens (see [C]) are not shown.(C) Schematic diagram of the interactions between AMPPNP and D2. Water molecules are indicated by “W.” Hydrogen and Mg^2PLUSPUSSIGN coordination bonds are indicated with dashed lines. Main-chain amide and carbonyl oxygen groups that interact with the ligand are shown emanating from the box surrounding the residue name, and side chain functionalities are shown schematically. Nonpolar van der Waals contacts are indicated by arcs. In (B) and (C), the asterisk at Lys-639 designates that this residue comes from an adjacent protomer in the D2 hexamer. This lysine appears to be only partially occupied, and its interaction with Oγ of AMPPNP is likely replaced by a water molecule in a fraction of the molecules in the crystal (see text).

PROCHECK

	Headers