PDBsum entry 1ksh

Signaling protein/hydrolase

PDB id: 1ksh

Contents

Protein chains

165 a.a. *

142 a.a. *

Ligands

PO4

GDP

Metals

_MG

Waters ×124

* Residue conservation analysis

PDB id:

1ksh

Name:

Signaling protein/hydrolase

Title:

Complex of arl2 and pde delta, crystal form 2 (native)

Structure:

Arf-like protein 2. Chain: a. Engineered: yes. Mutation: yes. Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase delta-subunit. Chain: b. Synonym: gmp-pde delta, p17 protein. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: arl2. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.244 R-free: 0.271

Authors:

M.Hanzal-Bayer,L.Renault,P.Roversi,A.Wittinghofer,R.C.Hillig

Key ref:

M.Hanzal-Bayer et al. (2002). The complex of Arl2-GTP and PDE delta: from structure to function. EMBO J, 21, 2095-2106. PubMed id: 11980706 DOI: 10.1093/emboj/21.9.2095

Date:

13-Jan-02 Release date: 08-May-02

Protein chain

Q9D0J4  (ARL2_MOUSE) -  ADP-ribosylation factor-like protein 2 from Mus musculus

Seq: 184 a.a.

Struc: 165 a.a.*

Protein chain

O43924  (PDE6D_HUMAN) -  Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta from Homo sapiens

Seq: 150 a.a.

Struc: 142 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain B: E.C.3.1.4.17 - 3',5'-cyclic-nucleotide phosphodiesterase.
• Reaction: a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate + H⁺

nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate (Bound ligand (Het Group name = GDP) matches with 44.83% similarity) + H(+)

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

Added reference

DOI no: 10.1093/emboj/21.9.2095

EMBO J 21:2095-2106 (2002)

PubMed id: 11980706

The complex of Arl2-GTP and PDE delta: from structure to function.

M.Hanzal-Bayer, L.Renault, P.Roversi, A.Wittinghofer, R.C.Hillig.

ABSTRACT

Arf-like (Arl) proteins are close relatives of the Arf regulators of vesicular transport, but their function is unknown. Here, we present the crystal structure of full-length Arl2-GTP in complex with its effector PDE delta solved in two crystal forms (Protein Data Bank codes 1KSG, 1KSH and 1KSJ). Arl2 shows a dramatic conformational change from the GDP-bound form, which suggests that it is reversibly membrane associated. PDE delta is structurally closely related to RhoGDI and contains a deep empty hydrophobic pocket. Further experiments show that H-Ras, Rheb, Rho6 and G alpha(i1) interact with PDE delta and that, at least for H-Ras, the intact C-terminus is required. We suggest PDE delta to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE delta-mediated transport.

Selected figure(s)

Figure 3.
Figure 3 Overall view of Arl2-GTP:PDE and comparison with Rap1A-GppNHp:RafRBD and Cdc42-GDP:RhoGDI. (A) Ribbon diagram of the complex of Arl2-GTP and PDE , with color coding of Arl2 as in Figure 1B. (B) Complex of Rap1A-GppNHp and the Ras binding domain of Raf (Nassar et al., 1995). Color coding as in (A). (C) Complex of Cdc42-GDP and RhoGDI1 (Hoffman et al., 2000). Color coding as in (A). C-terminal geranylgeranyl modification is shown in light blue.

Figure 4.
Figure 4 The interface of Arl2 and PDE . (A) Stereo representation of a view along the − interface (Arl2- 2 and PDE - 7). (B) Schematic representation. Color coding as in Figure 3. Interactions as dotted lines. Residues are boxed, water molecules are represented by circles.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 2095-2106) copyright 2002.

Figures were selected by an automated process.