PDBsum entry 1gmi

Kinase

PDB id: 1gmi

Contents

Protein chain

135 a.a. *

Metals

_MG

Waters ×107

* Residue conservation analysis

PDB id:

1gmi

Name:

Kinase

Title:

Structure of the c2 domain from novel protein kinasE C epsilon

Structure:

Protein kinasE C, epsilon type. Chain: a. Fragment: c2 domain. Synonym: protein kinasE C, npkc-epsilon. Engineered: yes

Source:

Rattus rattus. Rat. Organism_taxid: 10117. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.70Å R-factor: 0.234 R-free: 0.262

Authors:

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

Key ref:

W.F.Ochoa et al. (2001). Structure of the C2 domain from novel protein kinase Cepsilon. A membrane binding model for Ca(2+)-independent C2 domains. J Mol Biol, 311, 837-849. PubMed id: 11518534 DOI: 10.1006/jmbi.2001.4910

Date:

14-Sep-01 Release date: 25-Oct-01

Protein chain

P09216  (KPCE_RAT) -  Protein kinase C epsilon type from Rattus norvegicus

Seq: 737 a.a.

Struc: 135 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: 10.1006/jmbi.2001.4910

J Mol Biol 311:837-849 (2001)

PubMed id: 11518534

Structure of the C2 domain from novel protein kinase Cepsilon. A membrane binding model for Ca(2+)-independent C2 domains.

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

ABSTRACT

Protein kinase Cepsilon (PKCepsilon) is a member of the novel PKCs which are activated by acidic phospholipids, diacylglycerol and phorbol esters, but lack the calcium dependence of classical PKC isotypes. The crystal structures of the C2 domain of PKCepsilon, crystallized both in the absence and in the presence of the two acidic phospholipids, 1,2-dicaproyl-sn-phosphatidyl-l-serine (DCPS) and 1,2-dicaproyl-sn-phosphatidic acid (DCPA), have now been determined at 2.1, 1.7 and 2.8 A resolution, respectively. The central feature of the PKCepsilon-C2 domain structure is an eight-stranded, antiparallel, beta-sandwich with a type II topology similar to that of the C2 domains from phospholipase C and from novel PKCdelta. Despite the similar topology, important differences are found between the structures of C2 domains from PKCs delta and epsilon, suggesting they be considered as different PKC subclasses. Site-directed mutagenesis experiments and structural changes in the PKCepsilon-C2 domain from crystals with DCPS or DCPA indicate, though phospholipids were not visible in these structures, that loops joining strands beta1-beta2 and beta5-beta6 participate in the binding to anionic membranes. The different behavior in membrane-binding and activation between PKCepsilon and classical PKCs appears to originate in localized structural changes, which include a major reorganization of the region corresponding to the calcium binding pocket in classical PKCs. A mechanism is proposed for the interaction of the PKCepsilon-C2 domain with model membranes that retains basic features of the docking of C2 domains from classical, calcium-dependent, PKCs.

Selected figure(s)

Figure 4.
Figure 4. Top region of the C2-domain b-sandwich from PKCe. (a) Superimposition of loops 1 and 3 from PKCe (magenta) with the structurally equivalents loops CBR1 and CBR3 from the Ca^2+-dependent C2 domain of PKCa (cyan). The two Ca ions identified in the crystal structure of the C2 domain of PKCa are depicted as green spheres. Three of the five aspartate residues conserved in classical PKCs were replaced in PKCe by residues Pro33, His85 and Ala87. The imidazole ring of His85 occupies the position corresponding to the active Ca ion. (b) Superimposition of loop 1 and loop 3 of PKCe onto the equivalent loops in PKCd. The relative disposition of the loops and the orientation of the side-chains within the pocket differs markedly between the two novel PKCs.

Figure 6.
Figure 6. (a) The docking of the PKCa-C2-Ca^2+-DCPS ternary complex onto a model membrane and (b) the superimposition of the structures from the PKCs C2 domains a and e suggest (c) a docking mechanism for PKCe-C2. In this model only loop 3 appears to penetrate into the lipid bilayer, though loop 1 would also be in close contact with the membrane. In the model bulky side-chains of Trp23, Ile89 and Tyr91 (explicitly depicted) could reach the inner membrane while conserved basic residues (particularly Arg26, Arg32, Arg50 and probably also His85) would interact with the phospholipid charged heads (c). The coordination of the Mg2+ might also facilitate the interaction with the membrane (see the text). In this model the carboxy end of the C2 domain, to be continued by the pseudo-substrate and the C1 domain in the intact PKC, appears situated apart from the membrane.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 837-849) copyright 2001.

Figures were selected by an automated process.