PDBsum entry 1u29

Lipid binding protein

PDB id: 1u29

Contents

Protein chain

119 a.a. *

Ligands

I3P

Waters ×89

* Residue conservation analysis

PDB id:

1u29

Name:

Lipid binding protein

Title:

Triglycine variant of the arno pleckstrin homology domain in complex with ins(1,4,5)p3

Structure:

Cytohesin 2. Chain: a. Fragment: ph. Synonym: arf nucleotide-binding site opener, arno protein, clm2, sec7 homolog b, msec7-2. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: pscd2, sec7b. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.230 R-free: 0.262

Authors:

T.C.Cronin,J.P.Dinitto,M.P.Czech,D.G.Lambright

Key ref:

T.C.Cronin et al. (2004). Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains. EMBO J, 23, 3711-3720. PubMed id: 15359279 DOI: 10.1038/sj.emboj.7600388

Date:

16-Jul-04 Release date: 01-Feb-05

Protein chain

P63034  (CYH2_MOUSE) -  Cytohesin-2 from Mus musculus

Seq: 400 a.a.

Struc: 119 a.a.

DOI no: 10.1038/sj.emboj.7600388

EMBO J 23:3711-3720 (2004)

PubMed id: 15359279

Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains.

T.C.Cronin, J.P.DiNitto, M.P.Czech, D.G.Lambright.

ABSTRACT

The pleckstrin homology (PH) domains of the homologous proteins Grp1 (general receptor for phosphoinositides), ARNO (Arf nucleotide binding site opener), and Cytohesin-1 bind phosphatidylinositol (PtdIns) 3,4,5-trisphosphate with unusually high selectivity. Remarkably, splice variants that differ only by the insertion of a single glycine residue in the beta1/beta2 loop exhibit dual specificity for PtdIns(3,4,5)P(3) and PtdIns(4,5)P(2). The structural basis for this dramatic specificity switch is not apparent from the known modes of phosphoinositide recognition. Here, we report crystal structures for dual specificity variants of the Grp1 and ARNO PH domains in either the unliganded form or in complex with the head groups of PtdIns(4,5)P(2) and PtdIns(3,4,5)P(3). Loss of contacts with the beta1/beta2 loop with no significant change in head group orientation accounts for the significant decrease in PtdIns(3,4,5)P(3) affinity observed for the dual specificity variants. Conversely, a small increase rather than decrease in affinity for PtdIns(4,5)P(2) is explained by a novel binding mode, in which the glycine insertion alleviates unfavorable interactions with the beta1/beta2 loop. These observations are supported by a systematic mutational analysis of the determinants of phosphoinositide recognition.

Selected figure(s)

Figure 5.
Figure 5 Comparison with other PH domain structures. (A) Overlay of the 3G ARNO PH domain (semitransparent) and PLC PH domain (PDB ID code: 1MAI), both in complex with Ins(1,4,5)P[3], following superposition of C atoms. Ins(1,4,5)P[3]is depicted in red (3G ARNO) and yellow (PLC ). (B) Schematic diagram illustrating the approximate rigid body and torsion angle rotations that transform Ins(1,4,5)P[3] from the orientation in the PLC PH domain to that in the 3G ARNO PH domain. (C) Overlay of Ins(1,4,5)P[3] bound to the 3G ARNO PH domain with the electron density corresponding to inorganic sulfate ions from the unliganded 3G Grp1 PH domain following superposition of C atoms. The electron density is from A weighted F[o] -F[c] and 2F[o] -F[c] maps contoured at 3.0 and 1.2 , respectively. The maps were generated as in Figure 2C. (D) Overlay of the 2G Grp1 PH domain (semitransparent) and the PKB PH domain (PDB ID code: 1H10), both in complex with Ins(1,3,4,5)P[4], following superposition of C atoms. Ins(1,3,4,5)P[4] is depicted in yellow (2G Grp1) and green (PKB).

Figure 6.
Figure 6 Observed and hypothetical modes of polyphosphoinositide recognition. Schematic diagram depicting potential modes of polyphosphoinositide recognition by PH domains. The orientation of the inositol ring and disposition of phosphate groups are categorized with respect to the location of inorganic sulfate/phosphate ions observed in the unliganded structures of the 2G Grp1 and Dapp1 PH domains. Blue circles represent the phosphate binding site corresponding to the most buried and electropositive region of the head group binding site formed primarily by the N-terminal lysine and C-terminal arginine residue of the signature motif. Yellow circles represent the phosphate binding site comprised of the N-terminal lysine residue from the signature motif as well as basic and/or polar residues from the variable SDRs. In this classification of binding modes, rotational and/or translational displacements of the inositol ring that are not sufficiently large to alter the network of interactions with conserved residues are neglected as are the specific rotomer conformations of the phosphate groups.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 3711-3720) copyright 2004.

Figures were selected by an automated process.