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PDBsum entry 1bof

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protein ligands metals links
Signal transduction protein PDB id
1bof
Jmol
Contents
Protein chain
324 a.a. *
Ligands
SO4 ×2
GDP
Metals
_MG
Waters ×49
* Residue conservation analysis
PDB id:
1bof
Name: Signal transduction protein
Title: Gi-alpha-1 bound to gdp and magnesium
Structure: Gi alpha 1. Chain: a. Synonym: gia1, guanine nucleotide-binding protein g(i), alpha-1 subunit. Engineered: yes. Other_details: inactive form
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.227     R-free:   0.268
Authors: D.E.Coleman,S.R.Sprang
Key ref:
D.E.Coleman and S.R.Sprang (1998). Crystal structures of the G protein Gi alpha 1 complexed with GDP and Mg2+: a crystallographic titration experiment. Biochemistry, 37, 14376-14385. PubMed id: 9772163 DOI: 10.1021/bi9810306
Date:
04-Aug-98     Release date:   06-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10824  (GNAI1_RAT) -  Guanine nucleotide-binding protein G(i) subunit alpha-1
Seq:
Struc:
354 a.a.
324 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   11 terms 
  Biological process     cell cycle   7 terms 
  Biochemical function     nucleotide binding     11 terms  

 

 
DOI no: 10.1021/bi9810306 Biochemistry 37:14376-14385 (1998)
PubMed id: 9772163  
 
 
Crystal structures of the G protein Gi alpha 1 complexed with GDP and Mg2+: a crystallographic titration experiment.
D.E.Coleman, S.R.Sprang.
 
  ABSTRACT  
 
The effect of Mg2+ binding on the conformation of the inactive GDP-bound complex of the heterotrimeric G protein alpha subunit Gi alpha 1 has been investigated by X-ray crystallography. Crystal structures of the Gi alpha 1.GDP complex were determined after titration with 5, 10, 100, and 200 mM Mg2+. Comparison of these structures with that of the Mg2+-free complex revealed Mg2+ bound at the same site as observed in the structure of the active, Gi alpha 1. GTP gamma S.Mg2+-bound complex of Gi alpha 1, with a similar coordination scheme except for the substitution of a water molecule for an oxygen ligand of the gamma-phosphate of Gi alpha 1.GTP gamma S. Mg2+. In contrast to the GDP.Mg2+ complex of Gt alpha and of other G proteins, switch I residues of Gi alpha 1 participate in Mg2+ binding and undergo conformational changes as a consequence of Mg2+ binding. Partial order is induced in switch II, which is disordered in the Mg2+-free complex, but no order is observed in the switch III region. This contrasts with the GDP.Mg2+ complex of Gt alpha in which both switch II and III switch are ordered. Mg2+ binding also induces binding of an SO42- molecule to the active site in a manner which may mimic a Gi alpha 1.GDP.PO42-.Mg2+ product complex. Implications of these findings are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19899154 D.W.Sammond, Z.M.Eletr, C.Purbeck, and B.Kuhlman (2010).
Computational design of second-site suppressor mutations at protein-protein interfaces.
  Proteins, 78, 1055-1065.  
19222191 A.M.Preininger, M.A.Funk, W.M.Oldham, S.M.Meier, C.A.Johnston, S.Adhikary, A.J.Kimple, D.P.Siderovski, H.E.Hamm, and T.M.Iverson (2009).
Helix dipole movement and conformational variability contribute to allosteric GDP release in Galphai subunits.
  Biochemistry, 48, 2630-2642.
PDB code: 3d7m
19760664 H.E.Hamm, S.M.Meier, G.Liao, and A.M.Preininger (2009).
Trp fluorescence reveals an activation-dependent cation-pi interaction in the Switch II region of Galphai proteins.
  Protein Sci, 18, 2326-2335.  
18258741 A.R.Zurita, and L.Birnbaumer (2008).
The same mutation in Gsalpha and transducin alpha reveals behavioral differences between these highly homologous G protein alpha-subunits.
  Proc Natl Acad Sci U S A, 105, 2363-2368.  
  19513240 C.A.Johnston, M.D.Willard, A.J.Kimple, D.P.Siderovski, and F.S.Willard (2008).
A sweet cycle for Arabidopsis G-proteins: Recent discoveries and controversies in plant G-protein signal transduction.
  Plant Signal Behav, 3, 1067-1076.  
18249008 E.McCusker, and A.S.Robinson (2008).
Refolding of G protein alpha subunits from inclusion bodies expressed in Escherichia coli.
  Protein Expr Purif, 58, 342-355.  
17603074 D.W.Sammond, Z.M.Eletr, C.Purbeck, R.J.Kimple, D.P.Siderovski, and B.Kuhlman (2007).
Structure-based protocol for identifying mutations that enhance protein-protein binding affinities.
  J Mol Biol, 371, 1392-1404.
PDB code: 2om2
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.  
17053066 N.Van Eps, W.M.Oldham, H.E.Hamm, and W.L.Hubbell (2006).
Structural and dynamical changes in an alpha-subunit of a heterotrimeric G protein along the activation pathway.
  Proc Natl Acad Sci U S A, 103, 16194-16199.  
16004878 C.A.Johnston, F.S.Willard, M.R.Jezyk, Z.Fredericks, E.T.Bodor, M.B.Jones, R.Blaesius, V.J.Watts, T.K.Harden, J.Sondek, J.K.Ramer, and D.P.Siderovski (2005).
Structure of Galpha(i1) bound to a GDP-selective peptide provides insight into guanine nucleotide exchange.
  Structure, 13, 1069-1080.
PDB code: 1y3a
16051611 W.W.Ja, A.Adhikari, R.J.Austin, S.R.Sprang, and R.W.Roberts (2005).
A peptide core motif for binding to heterotrimeric G protein alpha subunits.
  J Biol Chem, 280, 32057-32060.  
14978301 C.Blouin, D.Butt, and A.J.Roger (2004).
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
  Protein Sci, 13, 608-616.  
15128951 C.J.Thomas, X.Du, P.Li, Y.Wang, E.M.Ross, and S.R.Sprang (2004).
Uncoupling conformational change from GTP hydrolysis in a heterotrimeric G protein alpha-subunit.
  Proc Natl Acad Sci U S A, 101, 7560-7565.
PDB codes: 1svk 1svs
14696184 P.J.Focia, H.Alam, T.Lu, U.D.Ramirez, and D.M.Freymann (2004).
Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh.
  Proteins, 54, 222-230.
PDB code: 1o87
15337739 V.Mittal, and M.E.Linder (2004).
The RGS14 GoLoco domain discriminates among Galphai isoforms.
  J Biol Chem, 279, 46772-46778.  
12399457 J.M.Manganello, J.S.Huang, T.Kozasa, T.A.Voyno-Yasenetskaya, and G.C.Le Breton (2003).
Protein kinase A-mediated phosphorylation of the Galpha13 switch I region alters the Galphabetagamma13-G protein-coupled receptor complex and inhibits Rho activation.
  J Biol Chem, 278, 124-130.  
11720992 R.Arimoto, O.G.Kisselev, G.M.Makara, and G.R.Marshall (2001).
Rhodopsin-transducin interface: studies with conformationally constrained peptides.
  Biophys J, 81, 3285-3293.  
10639138 P.Lin, T.Fischer, T.Weiss, and M.G.Farquhar (2000).
Calnuc, an EF-hand Ca(2+) binding protein, specifically interacts with the C-terminal alpha5-helix of G(alpha)i3.
  Proc Natl Acad Sci U S A, 97, 674-679.  
10494851 J.Müller, A.Marx, S.Sack, Y.H.Song, and E.Mandelkow (1999).
The structure of the nucleotide-binding site of kinesin.
  Biol Chem, 380, 981-992.  
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.