PDBsum entry: 1qu6

Transferase

PDB id: 1qu6

Contents

Protein chain

179 a.a. *

* Residue conservation analysis

PDB id:

1qu6

Name:

Transferase

Title:

Structure of the double-stranded RNA-binding domain of the protein kinase pkr reveals the molecular basis of its dsrna-mediated activation

Structure:

Protein kinase pkr. Chain: a. Fragment: dsrna-binding n-terminal domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

21 models

Authors:

S.Nanduri,B.W.Carpick,Y.Yang,B.R.G.Williams,J.Qin

Key ref:

S.Nanduri et al. (1998). Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation. EMBO J, 17, 5458-5465. PubMed id: 9736623 DOI: 10.1093/emboj/17.18.5458

Date:

08-Jul-99 Release date: 23-Dec-99

Protein chain

P19525  (E2AK2_HUMAN) -  Interferon-induced, double-stranded RNA-activated protein kinase

Seq: 551 a.a.

Struc: 179 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.10.2 - Non-specific protein-tyrosine kinase.
• Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
• Enzyme class 3: E.C.2.7.11.1 - Non-specific serine/threonine protein kinase.
• Reaction: ATP + a protein = ADP + a phosphoprotein

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biochemical function: RNA binding (2 terms)

reference

DOI no: 10.1093/emboj/17.18.5458

EMBO J 17:5458-5465 (1998)

PubMed id: 9736623

Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation.

S.Nanduri, B.W.Carpick, Y.Yang, B.R.Williams, J.Qin.

ABSTRACT

Protein kinase PKR is an interferon-induced enzyme that plays a key role in the control of viral infections and cellular homeostasis. Compared with other known kinases, PKR is activated by a distinct mechanism that involves double-stranded RNA (dsRNA) binding in its N-terminal region in an RNA sequence-independent fashion. We report here the solution structure of the 20 kDa dsRNA-binding domain (dsRBD) of human PKR, which provides the first three-dimensional insight into the mechanism of its dsRNA-mediated activation. The structure of dsRBD exhibits a dumb-bell shape comprising two tandem linked dsRNA-binding motifs (dsRBMs) both with an alpha-beta-beta-beta-alpha fold. The structure, combined with previous mutational and biochemical data, reveals a highly conserved RNA-binding site on each dsRBM and suggests a novel mode of protein-RNA recognition. The central linker is highly flexible, which may enable the two dsRBMs to wrap around the RNA duplex for cooperative and high-affinity binding, leading to the overall change of PKR conformation and its activation.

Selected figure(s)

Figure 4.
Figure 4 Backbone superpositions of dsRBM1 (red) and dsRBM2 (green) for PKR, and dsRBM (yellow) for Drosophila Staufen protein (Bycroft et al., 1995), showing the similar fold of the motifs. The side chains of potential RNA-binding residues in each dsRBM are displayed, most of which are well conserved among dsRBMs. The E.coli RNA III dsRBM also has similar folding topology (Kharrat et al., 1995) but its PDB coordinates were not available in the PDB for detailed comparison.

Figure 5.
Figure 5 Model of the interaction between the dsRBD and a 16 bp A form dsRNA helix. The model was built based on the following factors: (i) the RNA-binding sites are bulky and would bind to the minor groove without a substantial conformational change for the RNA duplex; (ii) dsRBD discriminates dsRNA over RNA -DNA and dsDNA, and specificity is due largely to molecular recognition of a network of 2'-OHs involving both strands of dsRNA (Bevilacqua and Cech, 1996); (iii) although dsRBD can bind as much as 30 -33 bp if the linker is straight, the biochemical data have shown that dsRBD covers 11 bp. In this mode, only exposed side chains in the putative binding site on both dsRBM1 and dsRBM2 were docked onto the minor groove of the RNA duplex to form hydrogen bonds with the 2'-OHs on both strands. Several positively charged Lys side chains, including the conserved K64-NH[3]^+ and K154-NH[3]^+, not only hydrogen-bond with the 2'-OHs but also make the electrostatic interactions with the neighboring phosphate oxygens (-OP1, pointing out to surface). Because the linker is long and highly flexible, the two dsRBMs contact >8 -11 bp by wrapping around the minor groove.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 5458-5465) copyright 1998.

Figures were selected by an automated process.