PDBsum entry 3llm

Hydrolase

PDB id: 3llm

Contents

Protein chains

235 a.a. *

Ligands

CAC

ADP ×2

GOL

Metals

_MN ×2

Waters ×27

* Residue conservation analysis

PDB id:

3llm

Name:

Hydrolase

Title:

Crystal structure analysis of a RNA helicase

Structure:

Atp-dependent RNA helicase a. Chain: a, b. Fragment: nucleotide binding domain (unp residues 329-563). Synonym: nuclear DNA helicase ii, ndh ii, deah box protein 9. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ddx9, dhx9, lkp, ndh2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.212 R-free: 0.238

Authors:

P.Schutz,T.Karlberg,R.Collins,C.H.Arrowsmith,H.Berglund,C.Bountra, S.Flodin,A.Flores,S.Graslund,M.Hammarstrom,A.Johansson,I.Johansson, A.Kallas,P.Kraulis,T.Kotenyova,A.Kotzsch,N.Markova,M.Moche, T.K.Nielsen,P.Nordlund,T.Nyman,C.Persson,A.K.Roos,M.I.Siponen, L.Svensson,A.G.Thorsell,L.Tresaugues,S.Van Den Berg,E.Wahlberg, J.Weigelt,M.Welin,M.Wisniewska,H.M.Schuler,Structural Genomics Consortium (Sgc)

Key ref:

P.Schütz et al. (2010). 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. PubMed id: 20510246

Date:

29-Jan-10 Release date: 12-May-10

Protein chains

Q08211  (DHX9_HUMAN) -  ATP-dependent RNA helicase A from Homo sapiens

Seq: 1270 a.a.

Struc: 235 a.a.

Enzyme reactions

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

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

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

reference

J Mol Biol 400:768-782 (2010)

PubMed id: 20510246

Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein.

P.Schütz, E.Wahlberg, T.Karlberg, M.Hammarström, R.Collins, A.Flores, H.Schüler.

ABSTRACT

RNA helicases of the DExD/H-box superfamily are critically involved in all RNA related processes. Previously, no crystal structures of human DExH-box domains had been determined, and their structures were difficult to predict owing to the low homology among DExH-motif containing proteins from diverse species. Here we present crystal structures of the conserved domains-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 MTAD 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, GTP, CTP, and UTP. Together, these findings allow 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.