PDBsum entry 2xb2

Hydrolase

PDB id: 2xb2

Contents

Protein chains

390 a.a. *

143 a.a. *

89 a.a. *

15 a.a. *

57 a.a. *

17 a.a. *

DNA/RNA

Ligands

ALA-GLU-ARG

ANP ×2

Metals

_MG ×2

* Residue conservation analysis

PDB id:

2xb2

Name:

Hydrolase

Title:

Crystal structure of the core mago-y14-eif4aiii-barentsz-upf3b assembly shows how the ejc is bridged to the nmd machinery

Structure:

Eukaryotic initiation factor 4a-iii. Chain: a, x. Synonym: eif4aiii, eukaryotic translation initiation factor 4a isoform 3, atp-dependent RNA helicase eif4a-3, atp-dependent RNA helicase ddx48, dead box protein 48, eukaryotic initiation factor 4a- like nuk-34, nuclear matrix protein 265, nmp 265. Engineered: yes. Protein mago nashi homolog. Chain: c, y.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

3.40Å R-factor: 0.220 R-free: 0.260

Authors:

G.Buchwald,J.Ebert,C.Basquin,J.Sauliere,U.Jayachandran,F.Bono,H.Le Hir,E.Conti

Key ref:

G.Buchwald et al. (2010). Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex. Proc Natl Acad Sci U S A, 107, 10050-10055. PubMed id: 20479275

Date:

03-Apr-10 Release date: 12-May-10

Protein chains

P38919  (IF4A3_HUMAN) -  Eukaryotic initiation factor 4A-III from Homo sapiens

Seq: 411 a.a.

Struc: 390 a.a.

Protein chains

P61326  (MGN_HUMAN) -  Protein mago nashi homolog from Homo sapiens

Seq: 146 a.a.

Struc: 143 a.a.

Protein chains

Q9Y5S9  (RBM8A_HUMAN) -  RNA-binding protein 8A from Homo sapiens

Seq: 174 a.a.

Struc: 89 a.a.

Protein chain

Q9BZI7  (REN3B_HUMAN) -  Regulator of nonsense transcripts 3B from Homo sapiens

Seq: 483 a.a.

Struc: 15 a.a.

Protein chains

O15234  (CASC3_HUMAN) -  Protein CASC3 from Homo sapiens

Seq: 703 a.a.

Struc: 57 a.a.

Protein chain

Q9BZI7  (REN3B_HUMAN) -  Regulator of nonsense transcripts 3B from Homo sapiens

Seq: 483 a.a.

Struc: 17 a.a.

DNA/RNA chains

U-U-U-U-U-U-U-U 8 bases

U-U-U-U-U-U-U 7 bases

Enzyme reactions

• Enzyme class 1: Chains A, X: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + phosphate + H(+)

• Enzyme class 2: Chains C, D, G, S, T, U, Y, Z: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

Proc Natl Acad Sci U S A 107:10050-10055 (2010)

PubMed id: 20479275

Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.

G.Buchwald, J.Ebert, C.Basquin, J.Sauliere, U.Jayachandran, F.Bono, H.Le Hir, E.Conti.

ABSTRACT

In mammals, Up-frameshift proteins (UPFs) form a surveillance complex that interacts with the exon junction complex (EJC) to elicit nonsense-mediated mRNA decay (NMD). UPF3b is the component of the surveillance complex that bridges the interaction with the EJC. Here, we report the 3.4 A resolution crystal structure of a minimal UPF3b-EJC assembly, consisting of the interacting domains of five proteins (UPF3b, MAGO, Y14, eIF4AIII, and Barentsz) together with RNA and adenylyl-imidodiphosphate. Human UPF3b binds with the C-terminal domain stretched over a composite surface formed by eIF4AIII, MAGO, and Y14. Residues that affect NMD when mutated are found at the core interacting surfaces, whereas differences between UPF3b and UPF3a map at peripheral interacting residues. Comparison with the binding mode of the protein PYM underscores how a common molecular surface of MAGO and Y14 recognizes different proteins acting at different times in the same pathway. The binding mode to eIF4AIII identifies a surface hot spot that is used by different DEAD-box proteins to recruit their regulators.