3LLM

Crystal Structure Analysis of a RNA Helicase

Summary for 3LLM

• Entry DOI: 10.2210/pdb3llm/pdb
• Descriptor: ATP-dependent RNA helicase A, MANGANESE (II) ION, CACODYLATE ION, ... (6 entities in total)
• Functional Keywords: alpha-beta-alpha, structural genomics, structural genomics consortium, sgc, activator, atp-binding, dna-binding, helicase, hydrolase, methylation, nucleotide-binding, nucleus, phosphoprotein, rna-binding
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus, nucleolus: Q08211
• Total number of polymer chains: 2
• Total formula weight: 54724.93

Authors

Schutz, P.,Karlberg, T.,Collins, R.,Arrowsmith, C.H.,Berglund, H.,Bountra, C.,Flodin, S.,Flores, A.,Graslund, S.,Hammarstrom, M.,Johansson, A.,Johansson, I.,Kallas, A.,Kraulis, P.,Kotenyova, T.,Kotzsch, A.,Markova, N.,Moche, M.,Nielsen, T.K.,Nordlund, P.,Nyman, T.,Persson, C.,Roos, A.K.,Siponen, M.I.,Svensson, L.,Thorsell, A.G.,Tresaugues, L.,Van Den Berg, S.,Wahlberg, E.,Weigelt, J.,Welin, M.,Wisniewska, M.,Schuler, H.M.,Structural Genomics Consortium (SGC) (deposition date: 2010-01-29, release date: 2010-05-12, Last modification date: 2024-11-27)

Primary citation

Schutz, P.,Wahlberg, E.,Karlberg, T.,Hammarstrom, M.,Collins, R.,Flores, A.,Schuler, H.
Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein.
J.Mol.Biol., 400:768-782, 2010

PubMed 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.

PubMed: 20510246
DOI: 10.1016/j.jmb.2010.05.046

Experimental method

X-RAY DIFFRACTION (2.8 Å)