PDBsum entry: 2acx

Transferase

PDB id: 2acx

Contents

Protein chains

495 a.a. *

Ligands

PO4 ×2

ANP ×2

Metals

_MG ×2

Waters ×37

* Residue conservation analysis

PDB id:

2acx

Name:

Transferase

Title:

Crystal structure of g protein coupled receptor kinase 6 bou amppnp

Structure:

G protein-coupled receptor kinase 6. Chain: a, b. Synonym: g protein-coupled receptor kinase grk6. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: grk6, gprk6. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: hi-9.

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.204 R-free: 0.243

Authors:

D.T.Lodowski,V.M.Tesmer,J.L.Benovic,J.J.Tesmer

Key ref:

D.T.Lodowski et al. (2006). The structure of G protein-coupled receptor kinase (GRK)-6 defines a second lineage of GRKs. J Biol Chem, 281, 16785-16793. PubMed id: 16613860 DOI: 10.1074/jbc.M601327200

Date:

19-Jul-05 Release date: 25-Apr-06

Protein chains

P43250  (GRK6_HUMAN) -  G protein-coupled receptor kinase 6

Seq: 576 a.a.

Struc: 495 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.7.11.16 - [G-protein-coupled receptor] kinase.
• Reaction: ATP + [G-protein-coupled receptor] = ADP + [G-protein-coupled receptor] phosphate

ATP + [G-protein-coupled receptor] = ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + [G-protein-coupled receptor] phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)
• Biological process: termination of G-protein coupled receptor signaling pathway (6 terms)
• Biochemical function: nucleotide binding (8 terms)

Added reference

DOI no: 10.1074/jbc.M601327200

J Biol Chem 281:16785-16793 (2006)

PubMed id: 16613860

The structure of G protein-coupled receptor kinase (GRK)-6 defines a second lineage of GRKs.

D.T.Lodowski, V.M.Tesmer, J.L.Benovic, J.J.Tesmer.

ABSTRACT

We describe the 2.6-A crystal structure of human G protein-coupled receptor kinase (GRK)-6, a key regulator of dopaminergic signaling and lymphocyte chemotaxis. GRK6 is a member of the GRK4 subfamily of GRKs, which is represented in most, if not all, metazoans. Comparison of GRK6 with GRK2 confirms that the catalytic core of all GRKs consists of intimately associated kinase and regulator of G protein signaling (RGS) homology domains. Despite being in complex with an ATP analog, the kinase domain of GRK6 remains in an open, presumably inactive conformation, suggesting that G protein-coupled receptors activate GRKs by inducing kinase domain closure. The structure reveals a putative phospholipid-binding site near the N terminus of GRK6 and structural elements within the kinase substrate channel that likely influence G protein-coupled receptor access and specificity. The crystalline GRK6 RGS homology domain forms an extensive dimer interface using conserved hydrophobic residues distinct from those in GRK2 that bind Galpha(q), although dimerization does not appear to occur in solution and is not required for receptor phosphorylation.

Selected figure(s)

Figure 1.
The asymmetric unit of the GRK6 crystals contains a homodimer formed via a conserved surface of the RH domain. Each GRK6 monomer consists of a bipartite RH domain containing 12α helices. The terminal subdomain (magenta) forms the crystalline dimer interface and consists of theα0–α3 andα8–α11 helices. The bundle subdomain forms an antiparallel four-helix bundle (dark purple) and consists of the remaining helices (α4–α7). The α1–α9 helices are homologous to those in the RH domains of RGS proteins. Compared with the structure of GRK2 (10), GRK6 has an additional N-terminal helix (α0) and shorter α5 and α11 helices. The GRK6 kinase domain (yellow α helices and orange β sheets) is composed of small and large lobes and is inserted between the α9 and α10 helices of the RH domain. Mg^2+·AMPPNP (spheres) is bound within each active site. Gray boxes correspond to regions magnified in the insets. Inset A, a polyvalent anion (modeled as P[i]) is bound to a putative phospholipid-binding site at the N terminus of GRK6 composed by residues from the α0 helix and the small lobe of the kinase domain. Density large enough for a tripeptide (shown with green carbons) also interacts with the anion. Potential hydrogen bonds and salt bridges are shown as dashed lines. Inset B, the RH dimer interface buries 2700 Å^2 of surface area. Residues that form the hydrophobic core of the interface are shown, including an interdigitated aromatic stack between the side chains of Tyr^166 and Phe^527 from each subunit. The backbone nitrogen and carbonyl groups of Phe^527 also form β sheet-like hydrogen bonds across the dimer interface. Nitrogen atoms are colored blue, oxygen red, phosphate green, and magnesium black. Carbon atoms are colored according to the domain in which they are found, except for those in AMPPNP, which are gray.

Figure 5.
The membrane-binding determinants in GRK6 and GRK2 are arranged similarly. GRK6 (A) and GRK2 (B) are expected to maintain similar orientations with respect to the membrane of the cell. For reference, IP[3] has been docked with the protein to demarcate the expected phospholipid-binding sites. In GRK6, the 5′-phosphate of IP[3] was superimposed on the polyvalent anion site observed in the crystal structure (Fig. 1). In GRK2, IP[3] was docked onto the PH domain using the structure of the phospholipase Cδ1 PH domain·IP[3] complex (Protein Data Bank code 1DJX) as a model. The C terminus of GRK6 is palmitoylated in the wild-type enzyme. Although it is disordered in our structure, it will be close to the expected membrane plane. Solvent-accessible surfaces of GRK6 (C) and GRK2 (D) are shown in the same orientation as in A. The surface is colored by the electrostatic potential (±3 kT/e^–). Both GRK6 and GRK2 have similar basic regions (blue) forming a flat surface that we believe will interact with the membrane plane. The αF–αG loop of GRK6, which occupies part of the peptide-binding channel and purportedly serves as a nuclear localization sequence (50), is also intensely basic, but below the expected membrane plane.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 16785-16793) copyright 2006.

Figures were selected by the author.