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PDBsum entry 1j8m

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protein links
Signaling protein PDB id
1j8m
Jmol
Contents
Protein chain
295 a.a. *
Waters ×159
* Residue conservation analysis
PDB id:
1j8m
Name: Signaling protein
Title: Signal recognition particle conserved gtpase domain from a. Ambivalens
Structure: Signal recognition 54 kda protein. Chain: f. Fragment: g-domain, gtpase domain. Synonym: srp54. Engineered: yes
Source: Acidianus ambivalens. Organism_taxid: 2283. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
2.00Å     R-factor:   0.219     R-free:   0.270
Authors: G.Montoya,K.Te Kaat,R.Moll,G.Schafer,I.Sinning
Key ref:
G.Montoya et al. (2000). The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex. Structure, 8, 515-525. PubMed id: 10801496 DOI: 10.1016/S0969-2126(00)00131-3
Date:
22-May-01     Release date:   13-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P70722  (SRP54_ACIAM) -  Signal recognition particle 54 kDa protein (Fragment)
Seq:
Struc:
451 a.a.
295 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     SRP-dependent cotranslational protein targeting to membrane   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1016/S0969-2126(00)00131-3 Structure 8:515-525 (2000)
PubMed id: 10801496  
 
 
The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex.
G.Montoya, K.Kaat, R.Moll, G.Schäfer, I.Sinning.
 
  ABSTRACT  
 
BACKGROUND: Protein targeting to the endoplasmic reticulum in eukaryotes and to the cell membrane in prokaryotes is mediated by the signal recognition particle (SRP) and its receptor (SR). Both contain conserved GTPase domains in the signal-peptide-binding proteins (SRP54 and Ffh) and the SR proteins (SRalpha and FtsY). These GTPases are involved in the regulation of protein targeting. Most studies so far have focussed on the SRP machinery of mammals and bacteria, leaving the SRP system of archaea less well understood. RESULTS: We report the crystal structure of the conserved GTPase (NG-Ffh) from the thermophilic archaeon Acidianus ambivalens at 2.0 A resolution and of the Thr112-->Ala mutant, which is inactive in GTP hydrolysis. This is the first structure of an SRP component from an archaeon and allows for a detailed comparison with related structures from Escherichia coli and thermophilic bacteria. In particular, differences in the conserved consensus regions for nucleotide binding and the subdomain interfaces are observed, which provide information about the regulation of the GTPase. These interactions allow us to propose a common signalling mechanism for the SRP-SR system. CONCLUSIONS: The overall structure of SRP-GTPases is well conserved between bacteria and archaea, which indicates strong similarities in the regulation of the SRP-targeting pathway. Surprisingly, structure comparisons identified a homodimeric ATP-binding protein as the closest relative. A heterodimer model for the SRP-SR interaction is presented.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Hydrophobic interactions close to the G4 region. A conserved hydrophobic core is formed by Ile4, Phe289, Phe284, Phe84, Met249, Leu259, Ile246 and Ile272.
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 515-525) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21255212 P.Kuhn, B.Weiche, L.Sturm, E.Sommer, F.Drepper, B.Warscheid, V.Sourjik, and H.G.Koch (2011).
The bacterial SRP receptor, SecA and the ribosome use overlapping binding sites on the SecY translocon.
  Traffic, 12, 563-578.  
  20672053 C.Zwieb, and S.Bhuiyan (2010).
Archaea signal recognition particle shows the way.
  Archaea, 2010, 485051.  
17186523 J.Gawronski-Salerno, J.S.Coon, P.J.Focia, and D.M.Freymann (2007).
X-ray structure of the T. aquaticus FtsY:GDP complex suggests functional roles for the C-terminal helix of the SRP GTPases.
  Proteins, 66, 984-995.
PDB code: 2iyl
17726013 L.Bahari, R.Parlitz, A.Eitan, G.Stjepanovic, E.S.Bochkareva, I.Sinning, and E.Bibi (2007).
Membrane targeting of ribosomes and their release require distinct and separable functions of FtsY.
  J Biol Chem, 282, 32168-32175.  
16755286 S.V.Albers, Z.Szabó, and A.J.Driessen (2006).
Protein secretion in the Archaea: multiple paths towards a unique cell surface.
  Nat Rev Microbiol, 4, 537-547.  
17139088 U.D.Ramirez, and D.M.Freymann (2006).
Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh.
  Acta Crystallogr D Biol Crystallogr, 62, 1520-1534.
PDB codes: 2j45 2j46
15542602 B.Zambelli, M.Stola, F.Musiani, K.De Vriendt, B.Samyn, B.Devreese, J.Van Beeumen, P.Turano, A.Dikiy, D.A.Bryant, and S.Ciurli (2005).
UreG, a chaperone in the urease assembly process, is an intrinsically unstructured GTPase that specifically binds Zn2+.
  J Biol Chem, 280, 4684-4695.  
15306407 A.Bolhuis (2004).
The archaeal Sec-dependent protein translocation pathway.
  Philos Trans R Soc Lond B Biol Sci, 359, 919-927.  
15189152 J.A.Doudna, and R.T.Batey (2004).
Structural insights into the signal recognition particle.
  Annu Rev Biochem, 73, 539-557.  
15228518 K.Wild, K.R.Rosendal, and I.Sinning (2004).
A structural step into the SRP cycle.
  Mol Microbiol, 53, 357-363.  
15523481 K.Wild, M.Halic, I.Sinning, and R.Beckmann (2004).
SRP meets the ribosome.
  Nat Struct Mol Biol, 11, 1049-1053.  
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
14726591 P.J.Focia, I.V.Shepotinovskaya, J.A.Seidler, and D.M.Freymann (2004).
Heterodimeric GTPase core of the SRP targeting complex.
  Science, 303, 373-377.
PDB code: 1okk
12913112 E.C.Mandon, Y.Jiang, and R.Gilmore (2003).
Dual recognition of the ribosome and the signal recognition particle by the SRP receptor during protein targeting to the endoplasmic reticulum.
  J Cell Biol, 162, 575-585.  
12853463 K.Nagai, C.Oubridge, A.Kuglstatter, E.Menichelli, C.Isel, and L.Jovine (2003).
Structure, function and evolution of the signal recognition particle.
  EMBO J, 22, 3479-3485.  
  15803656 C.Zwieb, and J.Eichler (2002).
Getting on target: the archaeal signal recognition particle.
  Archaea, 1, 27-34.  
12244111 R.M.Cleverley, and L.M.Gierasch (2002).
Mapping the signal sequence-binding site on SRP reveals a significant role for the NG domain.
  J Biol Chem, 277, 46763-46768.  
11753431 Y.J.Sun, F.Forouhar, H.M.Li Hm, S.L.Tu, Y.H.Yeh, S.Kao, H.L.Shr, C.C.Chou, C.Chen, and C.D.Hsiao (2002).
Crystal structure of pea Toc34, a novel GTPase of the chloroplast protein translocon.
  Nat Struct Biol, 9, 95.
PDB code: 1h65
11239791 J.Eichler, and R.Moll (2001).
The signal recognition particle of Archaea.
  Trends Microbiol, 9, 130-136.  
11395422 R.J.Keenan, D.M.Freymann, R.M.Stroud, and P.Walter (2001).
The signal recognition particle.
  Annu Rev Biochem, 70, 755-775.  
11566135 S.Padmanabhan, and D.M.Freymann (2001).
The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.
  Structure, 9, 859-867.
PDB codes: 1jpj 1jpn
11123669 A.A.Herskovits, E.S.Bochkareva, and E.Bibi (2000).
New prospects in studying the bacterial signal recognition particle pathway.
  Mol Microbiol, 38, 927-939.  
10970849 B.Prakash, L.Renault, G.J.Praefcke, C.Herrmann, and A.Wittinghofer (2000).
Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.
  EMBO J, 19, 4555-4564.
PDB code: 1f5n
10848955 J.Eichler (2000).
Archaeal protein translocation crossing membranes in the third domain of life.
  Eur J Biochem, 267, 3402-3412.  
10896472 P.B.Rupert, and A.R.Ferré-D'amaré (2000).
SRPrises in RNA-protein recognition.
  Structure, 8, R99-104.  
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.