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PDBsum entry 1t34

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protein ligands metals Protein-protein interface(s) links
Signaling protein,membrane protein PDB id
1t34
Jmol
Contents
Protein chains
426 a.a. *
21 a.a. *
Ligands
NAG-NAG ×4
Metals
_CL ×2
* Residue conservation analysis
PDB id:
1t34
Name: Signaling protein,membrane protein
Title: Rotation mechanism for transmembrane signaling by the atrial natriuretic peptide receptor
Structure: Atrial natriuretic peptide receptor a. Chain: a, b. Fragment: hormone binding domain (residues 1-435). Synonym: anp-a. Anpra. Gc-a. Guanylate cyclase. Npr-a. Atri natriuretic peptide a-type receptor. Engineered: yes. Atrial natriuretic peptide factor. Chain: h. Fragment: residues 129-149.
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: npr1. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell: baby hampster kidney cells. Synthetic: yes. Other_details: this sequence occurs in rattus norvegicus
Biol. unit: Trimer (from PQS)
Resolution:
2.95Å     R-factor:   0.237     R-free:   0.269
Authors: H.Ogawa,Y.Qiu,C.M.Ogata,K.S.Misono
Key ref:
H.Ogawa et al. (2004). Crystal structure of hormone-bound atrial natriuretic peptide receptor extracellular domain: rotation mechanism for transmembrane signal transduction. J Biol Chem, 279, 28625-28631. PubMed id: 15117952 DOI: 10.1074/jbc.M313222200
Date:
23-Apr-04     Release date:   03-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P18910  (ANPRA_RAT) -  Atrial natriuretic peptide receptor 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1057 a.a.
426 a.a.
Protein chain
Pfam   ArchSchema ?
P01161  (ANF_RAT) -  Natriuretic peptides A
Seq:
Struc:
152 a.a.
21 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.4.6.1.2  - Guanylate cyclase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP = 3',5'-cyclic GMP + diphosphate
GTP
=
3',5'-cyclic GMP
Bound ligand (Het Group name = NAG)
matches with 48.00% similarity
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     integral to membrane   1 term 

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M313222200 J Biol Chem 279:28625-28631 (2004)
PubMed id: 15117952  
 
 
Crystal structure of hormone-bound atrial natriuretic peptide receptor extracellular domain: rotation mechanism for transmembrane signal transduction.
H.Ogawa, Y.Qiu, C.M.Ogata, K.S.Misono.
 
  ABSTRACT  
 
A cardiac hormone, atrial natriuretic peptide (ANP), plays a major role in blood pressure and volume regulation. ANP activities are mediated by a single span transmembrane receptor carrying intrinsic guanylate cyclase activity. ANP binding to its extracellular domain stimulates guanylate cyclase activity by an as yet unknown mechanism. Here we report the crystal structure of dimerized extracellular hormone-binding domain in complex with ANP. The structural comparison with the unliganded receptor reveals that hormone binding causes the two receptor monomers to undergo an intermolecular twist with little intramolecular conformational change. This motion produces a Ferris wheel-like translocation of two juxtamembrane domains in the dimer with essentially no change in the interdomain distance. This movement alters the relative orientation of the two domains by a shift equivalent to counterclockwise rotation of each by 24 degrees. These results suggest that transmembrane signaling by the ANP receptor is initiated via a hormone-induced rotation mechanism.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Crystal structures of ANPR with and without bound ANP. The ANPR is shown in ribbon model, ANP in space-filling model in green, and non-covalently bound chloride ions as magenta balls.
Figure 6.
FIG. 6. Quaternary structure change in dimerized ANPR caused by binding of ANP, and proposed rotation mechanism for transmembrane signaling. (a) Schematic illustration of ANPR movement induced by ANP binding. ANPR molecules are shown as cylinders. ANPR molecules in apo dimer (cyan cylinders) undergo a clockwise twist to the complex positions (orange cylinders), capturing ANP (green triangle). This movement causes translocation of the two juxtamembrane domains in opposite directions (arrows). (b) The two juxtamembrane domains are approximated by circles. Upon ANP binding, the juxtamembrane domains in the apo dimer (circles C[apo] in cyan) translate to the complex positions (circles C[com] in orange) with essentially no change in the inter-domain distance. The arrows in the circles exemplify parallel translocation. This motion produces a change in the relative orientation of two juxtamembrane domains that is equivalent to rotating each by 24° counter-clockwise (inset).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 28625-28631) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21375693 K.S.Misono, J.S.Philo, T.Arakawa, C.M.Ogata, Y.Qiu, H.Ogawa, and H.S.Young (2011).
Structure, signaling mechanism and regulation of the natriuretic peptide receptor guanylate cyclase.
  FEBS J, 278, 1818-1829.  
20713070 P.Rondard, C.Goudet, J.Kniazeff, J.P.Pin, and L.Prézeau (2011).
The complexity of their activation mechanism opens new possibilities for the modulation of mGlu and GABAB class C G protein-coupled receptors.
  Neuropharmacology, 60, 82-92.  
20966614 T.Yamane, N.Takemura, H.Inoue, S.Soeta, M.Oishi, and H.Amasaki (2011).
Preliminary immunohistochemical study of natriuretic peptide receptor localization in canine and feline heart.
  J Vet Med Sci, 73, 375-378.  
19901021 G.Bereta, B.Wang, P.D.Kiser, W.Baehr, G.F.Jang, and K.Palczewski (2010).
A functional kinase homology domain is essential for the activity of photoreceptor guanylate cyclase 1.
  J Biol Chem, 285, 1899-1908.  
  20066666 H.Ogawa, Y.Qiu, J.S.Philo, T.Arakawa, C.M.Ogata, and K.S.Misono (2010).
Reversibly bound chloride in the atrial natriuretic peptide receptor hormone-binding domain: possible allosteric regulation and a conserved structural motif for the chloride-binding site.
  Protein Sci, 19, 544-557.
PDB code: 3a3k
20456499 J.Schröter, R.P.Zahedi, M.Hartmann, B.Gassner, A.Gazinski, J.Waschke, A.Sickmann, and M.Kuhn (2010).
Homologous desensitization of guanylyl cyclase A, the receptor for atrial natriuretic peptide, is associated with a complex phosphorylation pattern.
  FEBS J, 277, 2440-2453.  
19461966 A.Ahier, P.Rondard, N.Gouignard, N.Khayath, S.Huang, J.Trolet, D.J.Donoghue, M.Gauthier, J.P.Pin, and C.Dissous (2009).
A new family of receptor tyrosine kinases with a venus flytrap binding domain in insects and other invertebrates activated by aminoacids.
  PLoS One, 4, e5651.  
19187227 H.Ogawa, Y.Qiu, L.Huang, S.W.Tam-Chang, H.S.Young, and K.S.Misono (2009).
Structure of the atrial natriuretic peptide receptor extracellular domain in the unbound and hormone-bound states by single-particle electron microscopy.
  FEBS J, 276, 1347-1355.  
19926516 J.Nickel, W.Sebald, J.C.Groppe, and T.D.Mueller (2009).
Intricacies of BMP receptor assembly.
  Cytokine Growth Factor Rev, 20, 367-377.  
19274732 K.L.Longenecker, Q.Ruan, E.H.Fry, S.C.Saldana, S.E.Brophy, P.L.Richardson, and S.Y.Tetin (2009).
Crystal structure and thermodynamic analysis of diagnostic mAb 106.3 complexed with BNP 5-13 (C10A).
  Proteins, 76, 536-547.
PDB code: 3e8u
19393286 P.Pattanaik, L.Fromondi, K.P.Ng, J.He, and F.van den Akker (2009).
Expression, purification, and characterization of the intra-cellular domain of the ANP receptor.
  Biochimie, 91, 888-893.  
18987130 T.Lauber, N.Tidten, I.Matecko, M.Zeeb, P.Rösch, and U.C.Marx (2009).
Design and characterization of a soluble fragment of the extracellular ligand-binding domain of the peptide hormone receptor guanylyl cyclase-C.
  Protein Eng Des Sel, 22, 1-7.  
18713751 M.Hartmann, B.V.Skryabin, T.Müller, A.Gazinski, J.Schröter, B.Gassner, V.O.Nikolaev, M.Bünemann, and M.Kuhn (2008).
Alternative splicing of the guanylyl cyclase-A receptor modulates atrial natriuretic peptide signaling.
  J Biol Chem, 283, 28313-28320.  
18461395 M.Nakachi, M.Matsumoto, P.M.Terry, R.L.Cerny, and H.Moriyama (2008).
Identification of guanylate cyclases and related signaling proteins in sperm tail from sea stars by mass spectrometry.
  Mar Biotechnol (NY), 10, 564-571.  
17277921 B.Burczynska, T.Duda, and R.K.Sharma (2007).
ATP signaling site in the ARM domain of atrial natriuretic factor receptor guanylate cyclase.
  Mol Cell Biochem, 301, 93.  
17429599 I.Pagel-Langenickel, J.Buttgereit, M.Bader, and T.H.Langenickel (2007).
Natriuretic peptide receptor B signaling in the cardiovascular system: protection from cardiac hypertrophy.
  J Mol Med, 85, 797-810.  
17545198 M.Klotzsche, D.Goeke, C.Berens, and W.Hillen (2007).
Efficient and exclusive induction of Tet repressor by the oligopeptide Tip results from co-variation of their interaction site.
  Nucleic Acids Res, 35, 3945-3952.  
17057343 B.Altermark, A.O.Smalås, N.P.Willassen, and R.Helland (2006).
The structure of Vibrio cholerae extracellular endonuclease I reveals the presence of a buried chloride ion.
  Acta Crystallogr D Biol Crystallogr, 62, 1387-1391.
PDB codes: 2g7e 2g7f
17054659 G.E.Woodard, J.Zhao, and J.A.Rosado (2006).
Different effect of ATP on ANP receptor guanylyl cyclase in spontaneously hypertensive and normotensive rats.
  Acta Physiol (Oxf), 188, 195-206.  
16262696 S.Joubert, C.Jossart, N.McNicoll, and A.De Léan (2005).
Atrial natriuretic peptide-dependent photolabeling of a regulatory ATP-binding site on the natriuretic peptide receptor-A.
  FEBS J, 272, 5572-5583.  
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.