PDBsum entry: 1vec

RNA binding protein

PDB id: 1vec

Contents

Protein chains

206 a.a. *

Ligands

TLA

Metals

_ZN

Waters ×325

* Residue conservation analysis

PDB id:

1vec

Name:

RNA binding protein

Title:

Crystal structure of the n-terminal domain of rck/p54, a human dead-box protein

Structure:

Atp-dependent RNA helicase p54. Chain: a, b. Fragment: n-terminal domain. Synonym: rck, dead-box protein 6. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: humrck. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.01Å R-factor: 0.198 R-free: 0.251

Authors:

K.Hogetsu,T.Matsui,Y.Yukihiro,M.Tanaka,T.Sato,T.Kumasaka, N.Tanaka

Key ref:

T.Matsui et al. (2006). Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes. Genes Cells, 11, 439-452. PubMed id: 16611246 DOI: 10.1111/j.1365-2443.2006.00951.x

Date:

29-Mar-04 Release date: 13-Apr-04

Protein chains

P26196  (DDX6_HUMAN) -  Probable ATP-dependent RNA helicase DDX6

Seq: 483 a.a.

Struc: 206 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

reference

DOI no: 10.1111/j.1365-2443.2006.00951.x

Genes Cells 11:439-452 (2006)

PubMed id: 16611246

Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes.

T.Matsui, K.Hogetsu, J.Usukura, T.Sato, T.Kumasaka, Y.Akao, N.Tanaka.

ABSTRACT

Human rck/p54, a product of the gene cloned at the breakpoint of t(11; 14) (q23;q32) chromosomal translocation on 11q23 in B-cell lymphoma, is a member of the DEAD-box RNA helicase family. Here, the crystal structure of Nc-rck/p54, the N-terminal core domain of rck/p54, revealed that the P-loop in motif I formed a closed conformation, which was induced by Asn131, a residue unique to the RCK subfamily. It appears that ATP does not bind to the P-loop. The results of dynamic light scattering revealed to ATP-induced conformational change of rck/p54. It was demonstrated that free rck/p54 is a distended molecule in solution, and that the approach between N-terminal core and C-terminal domains for ATP binding would be essential when unwinding RNA. The results from helicase assay using electron micrograph, ATP hydrolytic and luciferase assay showed that c-myc IRES RNA, whose secondary structure regulates IRES-dependant translation, was unwound by rck/p54 and indicated that it is a good substrate for rck/p54. Over-expression of rck/p54 in HeLa cells caused growth inhibition and cell cycle arrest at G2/M with down-regulation of c-myc expression. These findings altogether suggest that rck/p54 may affect the IRES-dependent translation of c-myc even in the cells.