3LLM: Crystal Structure Analysis Of A Rna Helicase

Citation:
Abstract
RNA helicases of the DExD/H-box superfamily are critically involved in all RNA-related processes. No crystal structures of human DExH-box domains had been determined previously, and their structures were difficult to predict owing to the low level of homology among DExH-motif-containing proteins from diverse species. Here we present the crystal structures of the conserved domain 1 of the DEIH-motif-containing helicase DHX9 and of the DEAD-box helicase DDX20. Both contain a RecA-like core, but DHX9 differs from DEAD-box proteins in the arrangement of secondary structural elements and is more similar to viral helicases such as NS3. The N-terminus of the DHX9 core contains two long alpha-helices that reside on the surface of the core without contributing to nucleotide binding. The RNA-polymerase-II-interacting minimal transactivation domain sequence forms an extended loop structure that resides in a hydrophobic groove on the surface of the DEIH domain. DHX9 lacks base-selective contacts and forms an unspecific but important stacking interaction with the base of the bound nucleotide, and our biochemical analysis confirms that the protein can hydrolyze ATP, guanosine 5'-triphosphate, cytidine 5'-triphosphate, and uridine 5'-triphosphate. Together, these findings allow the localization of functional motifs within the three-dimensional structure of a human DEIH helicase and show how these enzymes can bind nucleotide with high affinity in the absence of a Q-motif.
PDB ID: 3LLMDownload
MMDB ID: 82018
PDB Deposition Date: 2010/1/29
Updated in MMDB: 2010/08
Experimental Method:
x-ray diffraction
Resolution: 2.8  Å
Source Organism:
Similar Structures:
Biological Unit for 3LLM: dimeric; determined by author and by software (PISA)
Molecular Components in 3LLM
Label Count Molecule
Proteins (2 molecules)
2
Atp-dependent RNA Helicase a(Gene symbol: DHX9)
Molecule annotation
Chemicals (6 molecules)
1
2
2
1
3
2
4
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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