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PDBsum entry 1lvz

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Peptide binding protein PDB id
1lvz
Jmol
Contents
Protein chain
11 a.a.
PDB id:
1lvz
Name: Peptide binding protein
Title: Metarhodopsin ii bound structure of c-terminal peptide of alpha-subunit of transducin
Structure: Guanine nucleotide-binding protein g(t), alpha-1 subunit. Chain: a. Fragment: s2 peptide, residues 339-349. Synonym: transducin alpha-1 chain. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: gnat1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: B.W.Koenig,G.Kontaxis,D.C.Mitchell,J.M.Louis,B.J.Litman, A.Bax
Key ref:
B.W.Koenig et al. (2002). Structure and orientation of a G protein fragment in the receptor bound state from residual dipolar couplings. J Mol Biol, 322, 441-461. PubMed id: 12217702 DOI: 10.1016/S0022-2836(02)00745-3
Date:
30-May-02     Release date:   11-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04695  (GNAT1_BOVIN) -  Guanine nucleotide-binding protein G(t) subunit alpha-1
Seq:
Struc:
350 a.a.
11 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1016/S0022-2836(02)00745-3 J Mol Biol 322:441-461 (2002)
PubMed id: 12217702  
 
 
Structure and orientation of a G protein fragment in the receptor bound state from residual dipolar couplings.
B.W.Koenig, G.Kontaxis, D.C.Mitchell, J.M.Louis, B.J.Litman, A.Bax.
 
  ABSTRACT  
 
Residual dipolar couplings for a ligand that is in fast exchange between a free state and a state where it is bound to a macroscopically ordered membrane protein carry precise information on the structure and orientation of the bound ligand. The couplings originate in the bound state but can be detected on the free ligand using standard high resolution NMR. This approach is used to study an analog of the C-terminal undecapeptide of the alpha-subunit of the heterotrimeric G protein transducin when bound to photo-activated rhodopsin. Rhodopsin is the major constituent of disk-shaped membrane vesicles from rod outer segments of bovine retinas, which align spontaneously in the NMR magnet. Photo-activation of rhodopsin triggers transient binding of the peptide, resulting in measurable dipolar contributions to 1J(NH) and 1J(CH) splittings. These dipolar couplings report on the time-averaged orientation of bond vectors in the bound peptide relative to the magnetic field, i.e. relative to the membrane normal. Approximate distance restraints of the bound conformation were derived from transferred NOEs, as measured from the difference of NOESY spectra recorded prior to and after photo-activation. The N-terminal eight residues of the bound undecapeptide adopt a near-ideal alpha-helical conformation. The helix is terminated by an alpha(L) type C-cap, with Gly9 at the C' position in the center of the reverse turn. The angle between the helix axis and the membrane normal is 40 degrees (+/-4) degrees. Peptide protons that make close contact with the receptor are identified by analysis of the NOESY cross-relaxation pattern and include the hydrophobic C terminus of the peptide.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Stereodiagrams of the set of 20 lowest energy structures of the S2 peptide in the MII bound state, calculated (a) with and (b) without dipolar couplings. (c) Superposition of the two average structures from (a) and (b), shown as backbone ribbon diagrams, showing that the backbones of the two families of structures are virtually indistinguishable. For orientation of peptide relative to membrane normal, see Figure 11.
Figure 8.
Figure 8. Stereodiagram of the energy-minimized average structure of the S2 peptide in the MII-bound state. The N-terminal eight residues are represented by an a-helical ribbon. The C-terminal reverse open turn residues are shown as stick representation, with backbone NH and CO bonds in blue and red, respectively, and side-chains in cyan. Close proximity (2.1 Å) of the Ser8-Og and Leu10-HN indicate a stabilizing hydrogen bond (broken line). The program MOLMOL[95.] was used for making this Figure.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 441-461) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21420337 D.T.Murray, Y.Lu, T.A.Cross, and J.R.Quine (2011).
Geometry of kinked protein helices from NMR data.
  J Magn Reson, 210, 82-89.  
20708633 H.W.Choe, J.H.Park, Y.J.Kim, and O.P.Ernst (2011).
Transmembrane signaling by GPCRs: insight from rhodopsin and opsin structures.
  Neuropharmacology, 60, 52-57.  
20951674 S.Tapaneeyakorn, A.D.Goddard, J.Oates, C.L.Willis, and A.Watts (2011).
Solution- and solid-state NMR studies of GPCRs and their ligands.
  Biochim Biophys Acta, 1808, 1462-1475.  
21041664 J.A.Goncalves, K.South, S.Ahuja, E.Zaitseva, C.A.Opefi, M.Eilers, R.Vogel, P.J.Reeves, and S.O.Smith (2010).
Highly conserved tyrosine stabilizes the active state of rhodopsin.
  Proc Natl Acad Sci U S A, 107, 19861-19866.  
  20633362 J.A.Goncalves, S.Ahuja, S.Erfani, M.Eilers, and S.O.Smith (2010).
Structure and function of G protein-coupled receptors using NMR spectroscopy.
  Prog Nucl Magn Reson Spectrosc, 57, 159-180.  
20004206 V.Hornak, S.Ahuja, M.Eilers, J.A.Goncalves, M.Sheves, P.J.Reeves, and S.O.Smith (2010).
Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints.
  J Mol Biol, 396, 510-527.  
20491123 Y.Chen, Y.Wu, P.Henklein, X.Li, K.P.Hofmann, K.Nakanishi, and O.P.Ernst (2010).
A photo-cross-linking strategy to map sites of protein-protein interactions.
  Chemistry, 16, 7389-7394.  
  20161395 H.J.Kim, S.C.Howell, W.D.Van Horn, Y.H.Jeon, and C.R.Sanders (2009).
Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins.
  Prog Nucl Magn Reson Spectrosc, 55, 335-360.  
19359362 J.L.Ortega-Roldan, M.R.Jensen, B.Brutscher, A.I.Azuaga, M.Blackledge, and N.A.van Nuland (2009).
Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.
  Nucleic Acids Res, 37, e70.  
19228693 K.Kato-Takagaki, Y.Mizukoshi, Y.Yoshizawa, D.Akazawa, Y.Torii, K.Ono, R.Tanimura, I.Shimada, and H.Takahashi (2009).
Structural and Interaction Analysis of Glycoprotein VI-binding Peptide Selected from a Phage Display Library.
  J Biol Chem, 284, 10720-10727.  
19836958 K.P.Hofmann, P.Scheerer, P.W.Hildebrand, H.W.Choe, J.H.Park, M.Heck, and O.P.Ernst (2009).
A G protein-coupled receptor at work: the rhodopsin model.
  Trends Biochem Sci, 34, 540-552.  
19541654 P.Scheerer, M.Heck, A.Goede, J.H.Park, H.W.Choe, O.P.Ernst, K.P.Hofmann, and P.W.Hildebrand (2009).
Structural and kinetic modeling of an activating helix switch in the rhodopsin-transducin interface.
  Proc Natl Acad Sci U S A, 106, 10660-10665.  
19837984 Y.Kofuku, C.Yoshiura, T.Ueda, H.Terasawa, T.Hirai, S.Tominaga, M.Hirose, Y.Maeda, H.Takahashi, Y.Terashima, K.Matsushima, and I.Shimada (2009).
Structural basis of the interaction between chemokine stromal cell-derived factor-1/CXCL12 and its G-protein-coupled receptor CXCR4.
  J Biol Chem, 284, 35240-35250.  
18177734 M.Musial-Siwek, D.A.Kendall, and P.L.Yeagle (2008).
Solution NMR of signal peptidase, a membrane protein.
  Biochim Biophys Acta, 1778, 937-944.  
18818650 P.Scheerer, J.H.Park, P.W.Hildebrand, Y.J.Kim, N.Krauss, H.W.Choe, K.P.Hofmann, and O.P.Ernst (2008).
Crystal structure of opsin in its G-protein-interacting conformation.
  Nature, 455, 497-502.
PDB code: 3dqb
18456304 T.G.Wensel (2008).
Signal transducing membrane complexes of photoreceptor outer segments.
  Vision Res, 48, 2052-2061.  
18818642 T.W.Schwartz, and W.L.Hubbell (2008).
Structural biology: A moving story of receptors.
  Nature, 455, 473-474.  
18043707 W.M.Oldham, and H.E.Hamm (2008).
Heterotrimeric G protein activation by G-protein-coupled receptors.
  Nat Rev Mol Cell Biol, 9, 60-71.  
18077356 B.Knierim, K.P.Hofmann, O.P.Ernst, and W.L.Hubbell (2007).
Sequence of late molecular events in the activation of rhodopsin.
  Proc Natl Acad Sci U S A, 104, 20290-20295.  
17351008 C.M.Taylor, G.V.Nikiforovich, and G.R.Marshall (2007).
Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin.
  Biophys J, 92, 4325-4334.  
16815918 A.H.Geiser, M.K.Sievert, L.W.Guo, J.E.Grant, M.P.Krebs, D.Fotiadis, A.Engel, and A.E.Ruoho (2006).
Bacteriorhodopsin chimeras containing the third cytoplasmic loop of bovine rhodopsin activate transducin for GTP/GDP exchange.
  Protein Sci, 15, 1679-1690.  
16407202 C.L.Piscitelli, T.E.Angel, B.W.Bailey, P.Hargrave, E.A.Dratz, and C.M.Lawrence (2006).
Equilibrium between metarhodopsin-I and metarhodopsin-II is dependent on the conformation of the third cytoplasmic loop.
  J Biol Chem, 281, 6813-6825.
PDB code: 1xgy
16826539 C.R.Sanders, and F.Sönnichsen (2006).
Solution NMR of membrane proteins: practice and challenges.
  Magn Reson Chem, 44, S24-S40.  
17177891 M.A.Anderson, B.Ogbay, O.G.Kisselev, D.P.Cistola, and G.R.Marshall (2006).
Alternate binding mode of C-terminal phenethylamine analogs of G(t)alpha(340-350) to photoactivated rhodopsin.
  Chem Biol Drug Des, 68, 295-307.  
16114100 M.J.Slusarz, A.Giełdoń, R.Slusarz, and J.Ciarkowski (2006).
Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors-molecular dynamics study of the activated receptor-vasopressin-G(alpha) systems.
  J Pept Sci, 12, 180-189.  
16114099 M.J.Slusarz, R.Slusarz, and J.Ciarkowski (2006).
Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin-modeling of an activated state.
  J Pept Sci, 12, 171-179.  
16333859 M.J.Slusarz, R.Slusarz, and J.Ciarkowski (2006).
Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: molecular dynamics simulation of the agonist-bound state in the membrane-aqueous system.
  Biopolymers, 81, 321-338.  
16142831 D.Fischer, and A.Geyer (2005).
NMR spectroscopic characterization of the membrane affinity of polyols.
  Magn Reson Chem, 43, 893-901.  
15889287 J.Ciarkowski, M.Witt, and R.Slusarz (2005).
A hypothesis for GPCR activation.
  J Mol Model, 11, 407-415.  
15983037 L.L.Anderson, G.R.Marshall, E.Crocker, S.O.Smith, and T.J.Baranski (2005).
Motion of carboxyl terminus of Galpha is restricted upon G protein activation. A solution NMR study using semisynthetic Galpha subunits.
  J Biol Chem, 280, 31019-31026.  
15898053 S.Albrizio, G.Caliendo, G.D'Errico, E.Novellino, P.Rovero, and A.M.D'Ursi (2005).
Galphas protein C-terminal alpha-helix at the interface: does the plasma membrane play a critical role in the Galphas protein functionality?
  J Pept Sci, 11, 617-626.  
15070895 J.M.Janz, and D.L.Farrens (2004).
Rhodopsin activation exposes a key hydrophobic binding site for the transducin alpha-subunit C terminus.
  J Biol Chem, 279, 29767-29773.  
15251227 K.Kristiansen (2004).
Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function.
  Pharmacol Ther, 103, 21-80.  
15041649 T.Huber, A.V.Botelho, K.Beyer, and M.F.Brown (2004).
Membrane model for the G-protein-coupled receptor rhodopsin: hydrophobic interface and dynamical structure.
  Biophys J, 86, 2078-2100.  
14500871 A.T.Alexandrescu, and R.A.Kammerer (2003).
Structure and disorder in the ribonuclease S-peptide probed by NMR residual dipolar couplings.
  Protein Sci, 12, 2132-2140.  
14525988 J.E.Slessareva, H.Ma, K.M.Depree, L.A.Flood, H.Bae, T.M.Cabrera-Vera, H.E.Hamm, and S.G.Graber (2003).
Closely related G-protein-coupled receptors use multiple and distinct domains on G-protein alpha-subunits for selective coupling.
  J Biol Chem, 278, 50530-50536.  
13678959 K.D.Ridge, N.G.Abdulaev, M.Sousa, and K.Palczewski (2003).
Phototransduction: crystal clear.
  Trends Biochem Sci, 28, 479-487.  
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.