PDBsum entry 3fmp

Oncoprotein/hydrolase

PDB id: 3fmp

Contents

Protein chains

420 a.a. *

229 a.a. *

Ligands

ADP ×2

* Residue conservation analysis

PDB id:

3fmp

Name:

Oncoprotein/hydrolase

Title:

Crystal structure of the nucleoporin nup214 in complex with the dead- box helicase ddx19

Structure:

Nuclear pore complex protein nup214. Chain: a, c. Synonym: nucleoporin nup214, 214 kda nucleoporin, protein can. Engineered: yes. Atp-dependent RNA helicase ddx19b. Chain: b, d. Synonym: dead box protein 19b, dead box RNA helicase dead5. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: nup214, cain, can, kiaa0023. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ddx19b, dbp5, ddx19. Expression_system_taxid: 562

Resolution:

3.19Å R-factor: 0.251 R-free: 0.283

Authors:

J.Napetschnig,E.W.Debler,G.Blobel,A.Hoelz

Key ref:

J.Napetschnig et al. (2009). Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19. Proc Natl Acad Sci U S A, 106, 3089-3094. PubMed id: 19208808 DOI: 10.1073/pnas.0813267106

Date:

22-Dec-08 Release date: 19-May-09

Protein chains

P35658  (NU214_HUMAN) -  Nuclear pore complex protein Nup214 from Homo sapiens

Seq: 2090 a.a.

Struc: 420 a.a.

Protein chains

Q9UMR2  (DD19B_HUMAN) -  ATP-dependent RNA helicase DDX19B from Homo sapiens

Seq: 479 a.a.

Struc: 229 a.a.

Enzyme reactions

• Enzyme class: Chains B, D: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0813267106

Proc Natl Acad Sci U S A 106:3089-3094 (2009)

PubMed id: 19208808

Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19.

J.Napetschnig, S.A.Kassube, E.W.Debler, R.W.Wong, G.Blobel, A.Hoelz.

ABSTRACT

Key steps in the export of mRNA from the nucleus to the cytoplasm are the transport through the nuclear pore complex (NPC) and the subsequent remodeling of messenger RNA-protein (mRNP) complexes that occurs at the cytoplasmic side of the NPC. Crucial for these events is the recruitment of the DEAD-box helicase Ddx19 to the cytoplasmic filaments of the NPC that is mediated by the nucleoporin Nup214. Here, we present the crystal structure of the Nup214 N-terminal domain in complex with Ddx19 in its ADP-bound state at 2.5 A resolution. Strikingly, the interaction surfaces are not only evolutionarily conserved but also exhibit strongly opposing surface potentials, with the helicase surface being positively and the Nup214 surface being negatively charged. We speculate that the positively charged surface of the interacting ADP-helicase binds competitively to a segment of mRNA of a linearized mRNP, passing through the NPC on its way to the cytoplasm. As a result, the ADP-helicase would dissociate from Nup214 and replace a single bound protein from the mRNA. One cycle of protein replacement would be accompanied, cooperatively, by nucleotide exchange, ATP hydrolysis, release of the ADP-helicase from mRNA and its rebinding to Nup214. Repeat of these cycles would remove proteins from a mRNP, one at a time, akin to a ratchet mechanism for mRNA export.

Selected figure(s)

Figure 1.
The 6D7A loop of the Nup214 NTD is essential for Ddx19 binding. (A) Domain organization of Nup214 and Ddx19. For Ddx19, the N-terminal extension (NTE, orange) and the 2 RecA-like domains (domain 1 and 2, green and light orange) are indicated. For Nup214, the β-propeller domain (light blue) and its C-terminal extension (CTE, yellow), the coiled-coil domain (gray), and the C-terminal unstructured region containing numerous FG-repeats (white) are indicated. The Nup214 NTD is composed of the β-propeller domain followed by the CTE. The bars above the domain structures mark the fragments of the orthorhombic crystal form. (B) Gel filtration profiles of full-length wild-type Ddx19 incubated with the Nup214 NTD, Nup214 NTD 1–405, or Nup214 NTD Δ6D7A before injection.

Figure 2.
Overview of the Nup214 NTD·Ddx19 NTD structure. Ribbon representation of the Nup214 NTD·Ddx19 NTD complex (Upper). A 90° rotated view is shown in Lower. For the Nup214 NTD, the β-propeller domain (blue), the 6D7A loop (magenta), the C-terminal extension (CTE; yellow), and the blade numbers are indicated. For the Ddx19 NTD, the N-terminal RecA-like domain (green) and the unique N-terminal extension (NTE; orange) is indicated. The ADP molecule bound to the Ddx19 NTD is shown in ball-and-stick representation.

Figures were selected by an automated process.