Crystal structure of human RNA helicase A (DHX9) : structural basis for unselective nucleotide base binding in a DEAD-box variant protein
Schütz, Patrick ; Wahlberg, Elisabet ; Karlberg, Tobias LU ; Hammarström, Martin ; Collins, Ruairi ; Flores, Alex and Schüler, Herwig LU
(2010)
In Journal of Molecular Biology
400(4).
p.82-768
- 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... (More)
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.
(Less)
- author
- Schütz, Patrick
; Wahlberg, Elisabet
; Karlberg, Tobias
LU
; Hammarström, Martin
; Collins, Ruairi
; Flores, Alex
and Schüler, Herwig
LU
- publishing date
- 2010-07-23
- type
- Contribution to journal
- publication status
- published
- keywords
- Amino Acid Sequence, Crystallography, X-Ray, DEAD Box Protein 20/chemistry, DEAD-box RNA Helicases/chemistry, Humans, Models, Molecular, Molecular Sequence Data, Neoplasm Proteins/chemistry, Nucleotides/metabolism, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Alignment
- in
- Journal of Molecular Biology
- volume
- 400
- issue
- 4
- pages
- 15 pages
- publisher
- Elsevier
- external identifiers
-
- scopus:77954384372
- pmid:20510246
- ISSN
- 1089-8638
- DOI
- 10.1016/j.jmb.2010.05.046
- language
- English
- LU publication?
- no
- additional info
- Copyright (c) 2010 Elsevier Ltd. All rights reserved.
- id
- bbf1bf2f-a6ab-4a47-9ccc-38ce1e4be94c
- date added to LUP
- 2024-11-21 18:00:49
- date last changed
- 2025-01-03 07:45:39
@article{bbf1bf2f-a6ab-4a47-9ccc-38ce1e4be94c,
abstract = {{<p>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.</p>}},
author = {{Schütz, Patrick and Wahlberg, Elisabet and Karlberg, Tobias and Hammarström, Martin and Collins, Ruairi and Flores, Alex and Schüler, Herwig}},
issn = {{1089-8638}},
keywords = {{Amino Acid Sequence; Crystallography, X-Ray; DEAD Box Protein 20/chemistry; DEAD-box RNA Helicases/chemistry; Humans; Models, Molecular; Molecular Sequence Data; Neoplasm Proteins/chemistry; Nucleotides/metabolism; Protein Structure, Secondary; Protein Structure, Tertiary; Sequence Alignment}},
language = {{eng}},
month = {{07}},
number = {{4}},
pages = {{82--768}},
publisher = {{Elsevier}},
series = {{Journal of Molecular Biology}},
title = {{Crystal structure of human RNA helicase A (DHX9) : structural basis for unselective nucleotide base binding in a DEAD-box variant protein}},
url = {{http://dx.doi.org/10.1016/j.jmb.2010.05.046}},
doi = {{10.1016/j.jmb.2010.05.046}},
volume = {{400}},
year = {{2010}},
}