PDBsum entry 1bdy

Calcium-binding

PDB id: 1bdy

Contents

Protein chains

123 a.a. *

Waters ×246

* Residue conservation analysis

PDB id:

1bdy

Name:

Calcium-binding

Title:

C2 domain from protein kinasE C delta

Structure:

Protein kinasE C. Chain: a, b. Fragment: c2-domain. Synonym: pkc. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.198 R-free: 0.247

Authors:

H.Pappa,J.Murray-Rust,L.V.Dekker,P.J.Parker,N.Q.Mcdonald

Key ref:

H.Pappa et al. (1998). Crystal structure of the C2 domain from protein kinase C-delta. Structure, 6, 885-894. PubMed id: 9687370 DOI: 10.1016/S0969-2126(98)00090-2

Date:

11-May-98 Release date: 14-Oct-98

Protein chains

P09215  (KPCD_RAT) -  Protein kinase C delta type from Rattus norvegicus

Seq: 673 a.a.

Struc: 123 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: 10.1016/S0969-2126(98)00090-2

Structure 6:885-894 (1998)

PubMed id: 9687370

Crystal structure of the C2 domain from protein kinase C-delta.

H.Pappa, J.Murray-Rust, L.V.Dekker, P.J.Parker, N.Q.McDonald.

ABSTRACT

BACKGROUND: The protein kinase C (PKC) family of lipid-dependent serine/theonine kinases plays a central role in many intracellular eukaryotic signalling events. Members of the novel (delta, epsilon, eta, theta) subclass of PKC isotypes lack the Ca2+ dependence of the conventional PKC isotypes and have an N-terminal C2 domain, originally defined as V0 (variable domain zero). Biochemical data suggest that this domain serves to translocate novel PKC family members to the plasma membrane and may influence binding of PKC activators. RESULTS: The crystal structure of PKC-delta C2 domain indicates an unusual variant of the C2 fold. Structural elements unique to this C2 domain include a helix and a protruding beta hairpin which may contribute basic sequences to a membrane-interaction site. The invariant C2 motif, Pro-X-Trp, where X is any amino acid, forms a short crossover loop, departing radically from its conformation in other C2 structures, and contains a tyrosine phosphorylation site unique to PKC-delta. This loop and two others adopt quite different conformations from the equivalent Ca(2+)-binding loops of phospholipase C-delta and synaptotagmin I, and lack sequences necessary for Ca2+ coordination. CONCLUSIONS: The N-terminal sequence of Ca(2+)-independent novel PKCs defines a divergent example of a C2 structure similar to that of phospholipase C-delta. The Ca(2+)-independent regulation of novel PKCs is explained by major structural and sequence differences resulting in three non-functional Ca(2+)-binding loops. The observed structural variation and position of a tyrosine-phosphorylation site suggest the existence of distinct subclasses of C2-like domains which may have evolved distinct functional roles and mechanisms to interact with lipid membranes.

Selected figure(s)

Figure 2.
Figure 2. Isomorphous and anomalous difference Fourier maps using selenomethionine data, superimposed on a backbone representation of the two molecules within the asymmetric unit. Experimental phases from the two mercury derivatives were used in map calculation; both maps are contoured at 5s. The ten selenium sites in the asymmetric unit are labelled according to the methionine residue number. (The figure was produced using the program SETOR [40].)

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 885-894) copyright 1998.

Figure was selected by an automated process.