PDBsum entry 2qkv

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Peptide binding protein PDB id
Jmol PyMol
Protein chains
92 a.a. *
Waters ×143
* Residue conservation analysis
PDB id:
Name: Peptide binding protein
Title: Crystal structure of the c645s mutant of the 5th pdz domain of inad
Structure: Inactivation-no-after-potential d protein. Chain: a, b. Fragment: 5th pdz domain. Engineered: yes. Mutation: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: inad. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.55Å     R-factor:   0.248     R-free:   0.267
Authors: R.Ranganathan,M.Socolich
Key ref:
P.Mishra et al. (2007). Dynamic scaffolding in a g protein-coupled signaling system. Cell, 131, 80-92. PubMed id: 17923089 DOI: 10.1016/j.cell.2007.07.037
11-Jul-07     Release date:   06-Nov-07    
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Protein chains
Pfam   ArchSchema ?
Q24008  (INAD_DROME) -  Inactivation-no-after-potential D protein
674 a.a.
92 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)


DOI no: 10.1016/j.cell.2007.07.037 Cell 131:80-92 (2007)
PubMed id: 17923089  
Dynamic scaffolding in a g protein-coupled signaling system.
P.Mishra, M.Socolich, M.A.Wall, J.Graves, Z.Wang, R.Ranganathan.
The INAD scaffold organizes a multiprotein complex that is essential for proper visual signaling in Drosophila photoreceptor cells. Here we show that one of the INAD PDZ domains (PDZ5) exists in a redox-dependent equilibrium between two conformations--a reduced form that is similar to the structure of other PDZ domains, and an oxidized form in which the ligand-binding site is distorted through formation of a strong intramolecular disulfide bond. We demonstrate transient light-dependent formation of this disulfide bond in vivo and find that transgenic flies expressing a mutant INAD in which PDZ5 is locked in the reduced state display severe defects in termination of visual responses and visually mediated reflex behavior. These studies demonstrate a conformational switch mechanism for PDZ domain function and suggest that INAD behaves more like a dynamic machine rather than a passive scaffold, regulating signal transduction at the millisecond timescale through cycles of conformational change.
  Selected figure(s)  
Figure 1.
Figure 1. Scaffolding in Drosophila Vision
(A) Scaffolding in Drosophila vision. Photon absorption by rhodopsin (1) sequentially activates Gqα (2), PLC-β (3), and TRP cation channels (4). Calcium influx (5) activates an eye-specific kinase (eye-PKC, 6) which phosphorylates the TRP channel (7) and the INAD scaffold (in red, 8). Through its PDZ domains, INAD assembles a core macromolecular complex involving PLC-β, TRP, and eye-PKC.
(B) Structural overlay of three previously characterized PDZ domains (PDB codes 1BE9, 1G9O, and 2F5Y).
(C) The atomic structure of PDZ5 shows overall similarity in the β sheets, but significant conformational changes in both α helices (see Figure S1 for quantitation). Examination of the 2F[o] − F[c] electron density at 1σ indicates the presence of a disulfide bond between cysteines 606 and 645.
(D) Sequence alignment of the PDZ domains shown. The color code corresponds to the structures in (B) and (C); the positions of the two cysteines are highlighted in the alignment.
Figure 3.
Figure 3. A Two-State Model for INAD PDZ5
A detailed view of the binding pocket in oxidized and reduced states of INAD PDZ5 (A) and in the C645S mutant structure (B). Key specificity-determining residues (F642 and F649) on the α2 helix adopt significantly different conformations in the oxidized and reduced states; the C645S mutant is effectively locked in the reduced state structure.
  The above figures are reprinted by permission from Cell Press: Cell (2007, 131, 80-92) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21262469 L.Deng, P.S.Kaeser, W.Xu, and T.C.Südhof (2011).
RIM proteins activate vesicle priming by reversing autoinhibitory homodimerization of Munc13.
  Neuron, 69, 317-331.  
  20052683 B.K.Ho, and D.A.Agard (2010).
Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility.
  Protein Sci, 19, 398-411.  
20509869 H.J.Lee, and J.J.Zheng (2010).
PDZ domains and their binding partners: structure, specificity, and modification.
  Cell Commun Signal, 8, 8.  
20648395 K.Nikolic, J.Loizu, P.Degenaar, and C.Toumazou (2010).
A stochastic model of the single photon response in Drosophila photoreceptors.
  Integr Biol (Camb), 2, 354-370.  
20949088 Q.S.Du, C.H.Wang, S.M.Liao, and R.B.Huang (2010).
Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain.
  PLoS One, 5, e13207.  
20485291 W.A.Lim (2010).
Designing customized cell signalling circuits.
  Nat Rev Mol Cell Biol, 11, 393-403.  
19623243 B.Katz, and B.Minke (2009).
Drosophila photoreceptors and signaling mechanisms.
  Front Cell Neurosci, 3, 2.  
19828436 C.M.Petit, J.Zhang, P.J.Sapienza, E.J.Fuentes, and A.L.Lee (2009).
Hidden dynamic allostery in a PDZ domain.
  Proc Natl Acad Sci U S A, 106, 18249-18254.  
19254957 H.Lu, H.T.Leung, N.Wang, W.L.Pak, and B.H.Shieh (2009).
Role of Ca2+/Calmodulin-dependent Protein Kinase II in Drosophila Photoreceptors.
  J Biol Chem, 284, 11100-11109.  
19837030 K.W.Yau, and R.C.Hardie (2009).
Phototransduction motifs and variations.
  Cell, 139, 246-264.  
19703402 N.Halabi, O.Rivoire, S.Leibler, and R.Ranganathan (2009).
Protein sectors: evolutionary units of three-dimensional structure.
  Cell, 138, 774-786.  
19252076 R.Bao, and M.Friedrich (2009).
Molecular evolution of the Drosophila retinome: exceptional gene gain in the higher Diptera.
  Mol Biol Evol, 26, 1273-1287.  
19359576 R.G.Smock, and L.M.Gierasch (2009).
Sending signals dynamically.
  Science, 324, 198-203.  
19011871 S.Frings (2009).
Primary processes in sensory cells: current advances.
  J Comp Physiol A Neuroethol Sens Neural Behav Physiol, 195, 1.  
  19892737 U.Dasgupta, T.Bamba, S.Chiantia, P.Karim, A.N.Tayoun, I.Yonamine, S.S.Rawat, R.P.Rao, K.Nagashima, E.Fukusaki, V.Puri, P.J.Dolph, P.Schwille, J.K.Acharya, and U.Acharya (2009).
Ceramide kinase regulates phospholipase C and phosphatidylinositol 4, 5, bisphosphate in phototransduction.
  Proc Natl Acad Sci U S A, 106, 20063-20068.  
19153575 W.Feng, and M.Zhang (2009).
Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density.
  Nat Rev Neurosci, 10, 87-99.  
18786361 C.H.Liu, A.K.Satoh, M.Postma, J.Huang, D.F.Ready, and R.C.Hardie (2008).
Ca2+-dependent metarhodopsin inactivation mediated by calmodulin and NINAC myosin III.
  Neuron, 59, 778-789.  
18339942 C.J.Bashor, N.C.Helman, S.Yan, and W.A.Lim (2008).
Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics.
  Science, 319, 1539-1543.  
18786382 M.J.Boulware, and J.S.Marchant (2008).
Timing in cellular Ca2+ signaling.
  Curr Biol, 18, R769-R776.  
18256265 N.Wang, H.T.Leung, W.L.Pak, Y.T.Carl, B.E.Wadzinski, and B.H.Shieh (2008).
Role of protein phosphatase 2A in regulating the visual signaling in Drosophila.
  J Neurosci, 28, 1444-1451.  
18280234 P.Herrlich, M.Karin, and C.Weiss (2008).
Supreme EnLIGHTenment: damage recognition and signaling in the mammalian UV response.
  Mol Cell, 29, 279-290.  
18007646 M.Zhang (2007).
Scaffold proteins as dynamic switches.
  Nat Chem Biol, 3, 756-757.  
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.