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PDBsum entry 2ju0

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protein metals Protein-protein interface(s) links
Metal binding protein/signaling protein PDB id
2ju0
Jmol
Contents
Protein chains
175 a.a. *
52 a.a. *
Metals
_CA ×3
* Residue conservation analysis
PDB id:
2ju0
Name: Metal binding protein/signaling protein
Title: Structure of yeast frequenin bound to pdtins 4-kinase
Structure: Calcium-binding protein ncs-1. Chain: a. Engineered: yes. Phosphatidylinositol 4-kinase pik1. Chain: b. Fragment: residues:121-174. Synonym: pi4-kinase, ptdins-4-kinase. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: frq1, ncs1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: pik1.
NMR struc: 15 models
Authors: J.Ames
Key ref:
T.Strahl et al. (2007). Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1). J Biol Chem, 282, 30949-30959. PubMed id: 17720810 DOI: 10.1074/jbc.M705499200
Date:
11-Aug-07     Release date:   28-Aug-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q06389  (NCS1_YEAST) -  Calcium-binding protein NCS-1
Seq:
Struc:
190 a.a.
175 a.a.
Protein chain
Pfam   ArchSchema ?
P39104  (PIK1_YEAST) -  Phosphatidylinositol 4-kinase PIK1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1066 a.a.
52 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: E.C.2.7.1.67  - 1-phosphatidylinositol 4-kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
1-Phosphatidyl-myo-inositol Metabolism
      Reaction: ATP + 1-phosphatidyl-1D-myo-inositol = ADP + 1-phosphatidyl-1D-myo- inositol 4-phosphate
ATP
+ 1-phosphatidyl-1D-myo-inositol
= ADP
+ 1-phosphatidyl-1D-myo- inositol 4-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     positive regulation of catalytic activity   2 terms 
  Biochemical function     protein binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M705499200 J Biol Chem 282:30949-30959 (2007)
PubMed id: 17720810  
 
 
Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1).
T.Strahl, I.G.Huttner, J.D.Lusin, M.Osawa, D.King, J.Thorner, J.B.Ames.
 
  ABSTRACT  
 
Yeast frequenin (Frq1), a small N-myristoylated EF-hand protein, activates phosphatidylinositol 4-kinase Pik1. The NMR structure of Ca2+-bound Frq1 complexed to an N-terminal Pik1 fragment (residues 121-174) was determined. The Frq1 main chain is similar to that in free Frq1 and related proteins in the same branch of the calmodulin superfamily. The myristoyl group and first eight residues of Frq1 are solvent-exposed, and Ca2+ binds the second, third, and fourth EF-hands, which associate to create a groove with two pockets. The Pik1 peptide forms two helices (125-135 and 156-169) connected by a 20-residue loop. Side chains in the Pik1 N-terminal helix (Val-127, Ala-128, Val-131, Leu-132, and Leu-135) interact with solvent-exposed residues in the Frq1 C-terminal pocket (Leu-101, Trp-103, Val-125, Leu-138, Ile-152, and Leu-155); side chains in the Pik1 C-terminal helix (Ala-157, Ala-159, Leu-160, Val-161, Met-165, and Met-167) contact solvent-exposed residues in the Frq1 N-terminal pocket (Trp-30, Phe-34, Phe-48, Ile-51, Tyr-52, Phe-55, Phe-85, and Leu-89). This defined complex confirms that residues in Pik1 pinpointed as necessary for Frq1 binding by site-directed mutagenesis are indeed sufficient for binding. Removal of the Pik1 N-terminal region (residues 8-760) from its catalytic domain (residues 792-1066) abolishes lipid kinase activity, inconsistent with Frq1 binding simply relieving an autoinhibitory constraint. Deletion of the lipid kinase unique motif (residues 35-110) also eliminates Pik1 activity. In the complex, binding of Ca2+-bound Frq1 forces the Pik1 chain into a U-turn. Frq1 may activate Pik1 by facilitating membrane targeting via the exposed N-myristoyl group and by imposing a structural transition that promotes association of the lipid kinase unique motif with the kinase domain.
 
  Selected figure(s)  
 
Figure 7.
FIGURE 7. Target binding to various EF-hand proteins. A, RK25 of rhodopsin kinase bound to recoverin (PDB code 2I94). B, Kv4.2N30 peptide derived from T1 domain of A-type voltage-gated K^+ channel bound to KChIP1 (PDB code 1S6C). C, Pik1-(121-174) peptide bound to Frq1 (PDB code 2JU0).
Figure 8.
FIGURE 8. Model of Pik1 activation by Frq1. A, schematic diagram of Pik1 primary structure in the absence of Frq1. LKU motif (residues 35-110) is in blue; Frq1-binding region (121-174) is in magenta, and catalytic (kinase) domain (residues 792-1066) is in green. B, schematic diagram of the structural rearrangement induced in Pik1 by binding of Ca^2+-bound Frq1. Bound Ca^2+-Frq1 imposes a U-turn in the main chain of Pik1, which we propose is necessary to allow the LKU domain (blue) to interact with the catalytic domain (green). In addition, N-myristoylation of Frq1 (red) helps targets the complex to the membranes that contain its substrate (PtdIns).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 30949-30959) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21077122 R.Tamuli, R.Kumar, and R.Deka (2011).
Cellular roles of neuronal calcium sensor-1 and calcium/calmodulin-dependent kinases in fungi.
  J Basic Microbiol, 51, 120-128.  
  21465563 X.Xu, R.Ishima, and J.B.Ames (2011).
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
  Proteins, 79, 1910-1922.  
19851889 S.Lim, and J.B.Ames (2009).
(1)H, (15)N, and (13)C chemical shift assignments of neuronal calcium sensor-1 homolog from fission yeast.
  Biomol NMR Assign, 3, 269-271.  
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