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PDBsum entry 1l7z
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protein ligands metals links
Metal binding protein/protein binding PDB id
1l7z

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
142 a.a. *
Ligands
GLY-GLY-LYS-LEU-
SER-LYS
MYR
Metals
_CA ×4
Waters ×75
* Residue conservation analysis
PDB id:
1l7z
Name: Metal binding protein/protein binding
Title: Crystal structure of ca2+/calmodulin complexed with myristoylated cap- 23/nap-22 peptide
Structure: Calmodulin. Chain: a. Engineered: yes. Cap-23/nap-22. Chain: b. Fragment: calmodulin binding domain. Synonym: acidic membrane protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: synthetic myristoylated peptide
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.239     R-free:   0.264
Authors: M.Matsubara,T.Nakatsu,E.Yamauchi,H.Kato,H.Taniguchi,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
M.Matsubara et al. (2004). Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin. EMBO J, 23, 712-718. PubMed id: 14765114 DOI: 10.1038/sj.emboj.7600093
Date:
18-Mar-02     Release date:   16-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0DP23  (CALM1_HUMAN) -  Calmodulin-1 from Homo sapiens
Seq:
Struc: 		149 a.a.
142 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/sj.emboj.7600093 EMBO J 23:712-718 (2004)
PubMed id: 14765114  
 
 
Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin.
M.Matsubara, T.Nakatsu, H.Kato, H.Taniguchi.
 
  ABSTRACT  
 
A variety of viral and signal transduction proteins are known to be myristoylated. Although the role of myristoylation in protein-lipid interaction is well established, the involvement of myristoylation in protein-protein interactions is less well understood. CAP-23/NAP-22 is a brain-specific protein kinase C substrate protein that is involved in axon regeneration. Although the protein lacks any canonical calmodulin (CaM)-binding domain, it binds CaM with high affinity. The binding of CAP-23/NAP-22 to CaM is myristoylation dependent and the N-terminal myristoyl group is directly involved in the protein-protein interaction. Here we show the crystal structure of Ca2+-CaM bound to a myristoylated peptide corresponding to the N-terminal domain of CAP-23/NAP-22. The myristoyl moiety of the peptide goes through a hydrophobic tunnel created by the hydrophobic pockets in the N- and C-terminal domains of CaM. In addition to the myristoyl group, several amino-acid residues in the peptide are important for CaM binding. This is a novel mode of binding and is very different from the mechanism of binding in other CaM-target complexes.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Binding interface of the myristoyl moiety of the mNAP peptide in the complex. (A) Electron density map of the myristoyl moiety. The simulated-annealing electron density map was refined by CNS (Brunger, 1998) and is contoured at 1.0 . The myristoyl moiety is shown in red. The figure was generated using TURBO-FRODO (Roussel and Cambillau, 1991). (B) Hydrophobic tunnel of CaM -mNAP peptide complex. The space model of the myristoyl moiety is shown in red, and the hydrophobic residues of CaM are shown in yellow. The figure was prepared with SPOCK (Christopher, 1998). (C) Stereo view of CaM residues within 5 Å of the myristoyl group as generated by MOLSCRIPT (Kraulis, 1991) and Raster3D (Merrit and Muphy, 1994). 		Figure 3.
Figure 3 Binding interface of specific residues in CaM with the mNAP peptide. (A) Stereo representation of the binding mode in the N-terminal protein domain generated by MOLSCRIPT (Kraulis, 1991) and Raster3D (Merrit and Muphy, 1994). The myristoylated peptide is indicated in purple, and the residues of CaM are shown in yellow. (B) Electrostatic surface of CaM colored by charge (red, negative; blue, positive), with the mNAP peptide shown in ribbon (green) representation. The figure was produced using GRASP (Nicholls et al, 1991).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 712-718) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20061304 M.Kato, N.Nagasaki-Takeuchi, Y.Ide, and M.Maeshima (2010).
An Arabidopsis hydrophilic Ca2(+) -binding protein with a PEVK-rich domain, PCaP2, is associated with the plasma membrane and interacts with calmodulin and phosphatidylinositol phosphates.
  Plant Cell Physiol, 51, 366-379.  
  21206729 M.Kato, N.Nagasaki-Takeuchi, Y.Ide, R.Tomioka, and M.Maeshima (2010).
PCaPs, possible regulators of PtdInsP signals on plasma membrane.
  Plant Signal Behav, 5, 848-850.  
  20448467 M.Kato, N.Nagasaki-Takeuchi, Y.Ide, R.Tomioka, and M.Maeshima (2010).
PCaPs, possible regulators of PtdInsP signals on plasma membrane.
  Plant Signal Behav, 5, 848-850.  
21081081 P.Bhagatji, R.Leventis, R.Rich, C.J.Lin, and J.R.Silvius (2010).
Multiple cellular proteins modulate the dynamics of K-ras association with the plasma membrane.
  Biophys J, 99, 3327-3335.  
20973648 V.Prokosch, C.Chiwitt, K.Rose, and S.Thanos (2010).
Deciphering proteins and their functions in the regenerating retina.
  Expert Rev Proteomics, 7, 775-795.  
19305019 D.A.Macdougall, S.Wachten, A.Ciruela, A.Sinz, and D.M.Cooper (2009).
Separate elements within a single IQ-like motif in adenylyl cyclase type 8 impart ca2+/calmodulin binding and autoinhibition.
  J Biol Chem, 284, 15573-15588.  
19297618 M.Hartl, A.Nist, M.I.Khan, T.Valovka, and K.Bister (2009).
Inhibition of Myc-induced cell transformation by brain acid-soluble protein 1 (BASP1).
  Proc Natl Acad Sci U S A, 106, 5604-5609.  
19404396 V.Majava, and P.Kursula (2009).
Domain swapping and different oligomeric States for the complex between calmodulin and the calmodulin-binding domain of calcineurin a.
  PLoS ONE, 4, e5402.
PDB code: 2w73
19560485 W.J.Tang, and Q.Guo (2009).
The adenylyl cyclase activity of anthrax edema factor.
  Mol Aspects Med, 30, 423-430.  
18182391 C.Lopez-Alcalá, B.Alvarez-Moya, P.Villalonga, M.Calvo, O.Bachs, and N.Agell (2008).
Identification of essential interacting elements in K-Ras/calmodulin binding and its role in K-Ras localization.
  J Biol Chem, 283, 10621-10631.  
18438920 I.Korshunova, P.Caroni, K.Kolkova, V.Berezin, E.Bock, and P.S.Walmod (2008).
Characterization of BASP1-mediated neurite outgrowth.
  J Neurosci Res, 86, 2201-2213.  
18397324 N.Nagasaki, R.Tomioka, and M.Maeshima (2008).
A hydrophilic cation-binding protein of Arabidopsis thaliana, AtPCaP1, is localized to plasma membrane via N-myristoylation and interacts with calmodulin and the phosphatidylinositol phosphates PtdIns(3,4,5)P(3) and PtdIns(3,5)P(2).
  FEBS J, 275, 2267-2282.  
18518982 N.V.Valeyev, D.G.Bates, P.Heslop-Harrison, I.Postlethwaite, and N.V.Kotov (2008).
Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach.
  BMC Syst Biol, 2, 48.  
16568447 A.Ganoth, E.Nachliel, R.Friedman, and M.Gutman (2006).
Molecular dynamics study of a calmodulin-like protein with an IQ peptide: spontaneous refolding of the protein around the peptide.
  Proteins, 64, 133-146.  
16844751 A.Ganoth, R.Friedman, E.Nachliel, and M.Gutman (2006).
A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides.
  Biophys J, 91, 2436-2450.  
16957918 F.Capozzi, F.Casadei, and C.Luchinat (2006).
EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view.
  J Biol Inorg Chem, 11, 949-962.  
16895919 H.Konishi, K.Tashiro, Y.Murata, H.Nabeshi, E.Yamauchi, and H.Taniguchi (2006).
CFBP is a novel tyrosine-phosphorylated protein that might function as a regulator of CIN85/CD2AP.
  J Biol Chem, 281, 28919-28931.  
16721661 K.Chen, J.Ruan, and L.A.Kurgan (2006).
Prediction of three dimensional structure of calmodulin.
  Protein J, 25, 57-70.  
17051234 M.D.Resh (2006).
Trafficking and signaling by fatty-acylated and prenylated proteins.
  Nat Chem Biol, 2, 584-590.  
16432210 M.Ikura, and J.B.Ames (2006).
Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality.
  Proc Natl Acad Sci U S A, 103, 1159-1164.  
15640140 H.Tapp, I.M.Al-Naggar, E.G.Yarmola, A.Harrison, G.Shaw, A.S.Edison, and M.R.Bubb (2005).
MARCKS is a natively unfolded protein with an inaccessible actin-binding site: evidence for long-range intramolecular interactions.
  J Biol Chem, 280, 9946-9956.  
16043511 M.Fivaz, and T.Meyer (2005).
Reversible intracellular translocation of KRas but not HRas in hippocampal neurons regulated by Ca2+/calmodulin.
  J Cell Biol, 170, 429-441.  
15650187 P.Gripon, I.Cannie, and S.Urban (2005).
Efficient inhibition of hepatitis B virus infection by acylated peptides derived from the large viral surface protein.
  J Virol, 79, 1613-1622.  
16138079 Q.Guo, Y.Shen, Y.S.Lee, C.S.Gibbs, M.Mrksich, and W.J.Tang (2005).
Structural basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin.
  EMBO J, 24, 3190-3201.
PDB codes: 1yrt 1yru 1zot 2col
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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