PDBsum entry 1dsy

Transferase

PDB id: 1dsy

Contents

Protein chain

137 a.a. *

Ligands

PO4

PSF

Metals

_CA ×2

Waters ×39

* Residue conservation analysis

PDB id:

1dsy

Name:

Transferase

Title:

C2 domain from protein kinasE C (alpha) complexed with ca2+ and phosphatidylserine

Structure:

Protein kinasE C, alpha type. Chain: a. Fragment: calcium/phospholipid binding domain. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.60Å R-factor: 0.195 R-free: 0.233

Authors:

N.Verdaguer,S.Corbalan-Garcia,W.F.Ochoa,I.Fita,J.C.Gomez-Fernandez

Key ref:

N.Verdaguer et al. (1999). Ca(2+) bridges the C2 membrane-binding domain of protein kinase Calpha directly to phosphatidylserine. EMBO J, 18, 6329-6338. PubMed id: 10562545 DOI: 10.1093/emboj/18.22.6329

Date:

10-Jan-00 Release date: 26-Jan-00

Protein chain

P05696  (KPCA_RAT) -  Protein kinase C alpha type from Rattus norvegicus

Seq: 672 a.a.

Struc: 137 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.11.13 - protein kinase C.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

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

reference

DOI no: 10.1093/emboj/18.22.6329

EMBO J 18:6329-6338 (1999)

PubMed id: 10562545

Ca(2+) bridges the C2 membrane-binding domain of protein kinase Calpha directly to phosphatidylserine.

N.Verdaguer, S.Corbalan-Garcia, W.F.Ochoa, I.Fita, J.C.Gómez-Fernández.

ABSTRACT

The C2 domain acts as a membrane-targeting module in a diverse group of proteins including classical protein kinase Cs (PKCs), where it plays an essential role in activation via calcium-dependent interactions with phosphatidylserine. The three-dimensional structures of the Ca(2+)-bound forms of the PKCalpha-C2 domain both in the absence and presence of 1, 2-dicaproyl-sn-phosphatidyl-L-serine have now been determined by X-ray crystallography at 2.4 and 2.6 A resolution, respectively. In the structure of the C2 ternary complex, the glycerophosphoserine moiety of the phospholipid adopts a quasi-cyclic conformation, with the phosphoryl group directly coordinated to one of the Ca(2+) ions. Specific recognition of the phosphatidylserine is reinforced by additional hydrogen bonds and hydrophobic interactions with protein residues in the vicinity of the Ca(2+) binding region. The central feature of the PKCalpha-C2 domain structure is an eight-stranded, anti-parallel beta-barrel with a molecular topology and organization of the Ca(2+) binding region closely related to that found in PKCbeta-C2, although only two Ca(2+) ions have been located bound to the PKCalpha-C2 domain. The structural information provided by these results suggests a membrane binding mechanism of the PKCalpha-C2 domain in which calcium ions directly mediate the phosphatidylserine recognition while the calcium binding region 3 might penetrate into the phospholipid bilayer.

Selected figure(s)

Figure 1.
Figure 1 (A) Overall structure of the C2 domain of PKC bound to PS. -strands are depicted as arrows numbered sequentially. The two Ca^2+ ions located in the calcium binding site are also shown as orange spheres. The DCPS and phosphate molecules found in the ternary complex are explicitly shown as balls and sticks. (B) Surface potential drawing of the PKC -C2 -Ca^2+ domain structure as computed and displayed by GRASP (Nicholls et al., 1991). Positively and negatively charged regions are shown in blue and red, respectively. The DCPS- and phosphate-bound molecules are also depicted as stick models.

Figure 3.
Figure 3 (A) Stereoviews of the F[o]-F[c] omit map of the ternary complex at 2.6 Å resolution, in the vicinity of Ca1 contoured at 2 . All the atoms corresponding to residues Asn189, Arg216, Arg249, Thr251 and also to the ion Ca1 and to the DCPS ligand were omitted for the map calculation according to the CNS protocols. The molecular fragments modeled into the corresponding density are also shown. The DCPS ligand is represented with the conformation corresponding to the sn-2 model (see the text). (B) Stereoviews, in the same orientation as in (A), of the F[o]-F[c] omit map (blue) of the ternary complex calculated omitting only the DCPS ligand. The residual F[o]-F[c] map calculated from the final refined model is also shown superimposed together with the DCPS model. Only some positive density (red) could be seen close to the position corresponding to the phosphoryl moiety. All the map contouring shown was carried out 2.5 . (C) The superimposition of the two alternative DCPS conformations (sn-1 in purple and sn-2 in green) emphasizes the similar atomic disposition.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 6329-6338) copyright 1999.

Figures were selected by an automated process.