spacer
spacer

PDBsum entry 1jpj

Go to PDB code: 
protein ligands links
Signaling protein PDB id
1jpj
Jmol
Contents
Protein chain
294 a.a. *
Ligands
GNP
Waters ×59
* Residue conservation analysis
PDB id:
1jpj
Name: Signaling protein
Title: Gmppnp complex of srp gtpase ng domain
Structure: Signal recognition particle protein. Chain: a. Fragment: ng domain. Synonym: fifty-four homolog. Engineered: yes
Source: Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.30Å     R-factor:   0.201     R-free:   0.306
Authors: S.Padmanabhan,D.M.Freymann
Key ref:
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. PubMed id: 11566135 DOI: 10.1016/S0969-2126(01)00641-4
Date:
02-Aug-01     Release date:   02-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O07347  (SRP54_THEAQ) -  Signal recognition particle protein
Seq:
Struc:
430 a.a.
294 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     signal recognition particle   1 term 
  Biological process     SRP-dependent cotranslational protein targeting to membrane   1 term 
  Biochemical function     nucleotide binding     4 terms  

 

 
DOI no: 10.1016/S0969-2126(01)00641-4 Structure 9:859-867 (2001)
PubMed id: 11566135  
 
 
The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.
S.Padmanabhan, D.M.Freymann.
 
  ABSTRACT  
 
BACKGROUND: The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein that mediates cotranslational targeting of secreted and membrane proteins to the membrane. Targeting is regulated by GTP binding and hydrolysis events that require direct interaction between structurally homologous "NG" GTPase domains of the SRP signal recognition subunit and its membrane-associated receptor, SR alpha. Structures of both the apo and GDP bound NG domains of the prokaryotic SRP54 homolog, Ffh, and the prokaryotic receptor homolog, FtsY, have been determined. The structural basis for the GTP-dependent interaction between the two proteins, however, remains unknown. RESULTS: We report here two structures of the NG GTPase of Ffh from Thermus aquaticus bound to the nonhydrolyzable GTP analog GMPPNP. Both structures reveal an unexpected binding mode in which the beta-phosphate is kinked away from the binding site and magnesium is not bound. Binding of the GTP analog in the canonical conformation found in other GTPase structures is precluded by constriction of the phosphate binding P loop. The structural difference between the Ffh complex and other GTPases suggests a specific conformational change that must accompany movement of the nucleotide from an "inactive" to an "active" binding mode. CONCLUSIONS: Conserved side chains of the GTPase sequence motifs unique to the SRP subfamily may function to gate formation of the active GTP bound conformation. Exposed hydrophobic residues provide an interaction surface that may allow regulation of the GTP binding conformation, and thus activation of the GTPase, during the association of SRP with its receptor.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. GMPPNP Binding to the NG DomainOmit difference (F[o] - F[c]) electron density maps contoured at 3 s (light blue) and 6 s (dark blue) for (a) structure N1 and (b) structure N2a. The triplet of electron-dense peaks to the right in each image indicates the positions of the phosphate groups. Two residues, Gln107 and Thr112, define the top and bottom of the P loop jaws

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 859-867) copyright 2001.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20544960 M.Yang, X.Zhang, and K.Han (2010).
Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations.
  Proteins, 78, 2222-2237.  
19469550 S.O.Shan, S.L.Schmid, and X.Zhang (2009).
Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases.
  Biochemistry, 48, 6696-6704.  
18931411 U.D.Ramirez, P.J.Focia, and D.M.Freymann (2008).
Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh.
  Acta Crystallogr D Biol Crystallogr, 64, 1043-1053.
PDB codes: 2c03 2c04
18617187 X.Zhang, S.Kung, and S.O.Shan (2008).
Demonstration of a multistep mechanism for assembly of the SRP x SRP receptor complex: implications for the catalytic role of SRP RNA.
  J Mol Biol, 381, 581-593.  
17622352 C.L.Reyes, E.Rutenber, P.Walter, and R.M.Stroud (2007).
X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates.
  PLoS ONE, 2, e607.
PDB codes: 2q9a 2q9b 2q9c
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
17475780 P.Jaru-Ampornpan, S.Chandrasekar, and S.O.Shan (2007).
Efficient interaction between two GTPases allows the chloroplast SRP pathway to bypass the requirement for an SRP RNA.
  Mol Biol Cell, 18, 2636-2645.  
17682051 S.O.Shan, S.Chandrasekar, and P.Walter (2007).
Conformational changes in the GTPase modules of the signal reception particle and its receptor drive initiation of protein translocation.
  J Cell Biol, 178, 611-620.  
17086205 C.Schaffitzel, M.Oswald, I.Berger, T.Ishikawa, J.P.Abrahams, H.K.Koerten, R.I.Koning, and N.Ban (2006).
Structure of the E. coli signal recognition particle bound to a translating ribosome.
  Nature, 444, 503-506.
PDB code: 2iy3
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.  
14749771 E.C.Mandon, and R.Gilmore (2004).
GTPase twins in the SRP family.
  Nat Struct Mol Biol, 11, 115-116.  
15189152 J.A.Doudna, and R.T.Batey (2004).
Structural insights into the signal recognition particle.
  Annu Rev Biochem, 73, 539-557.  
14724630 P.F.Egea, S.O.Shan, J.Napetschnig, D.F.Savage, P.Walter, and R.M.Stroud (2004).
Substrate twinning activates the signal recognition particle and its receptor.
  Nature, 427, 215-221.
PDB code: 1rj9
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
12663860 S.O.Shan, and P.Walter (2003).
Induced nucleotide specificity in a GTPase.
  Proc Natl Acad Sci U S A, 100, 4480-4485.  
11726508 Y.Lu, H.Y.Qi, J.B.Hyndman, N.D.Ulbrandt, A.Teplyakov, N.Tomasevic, and H.D.Bernstein (2001).
Evidence for a novel GTPase priming step in the SRP protein targeting pathway.
  EMBO J, 20, 6724-6734.  
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 codes are shown on the right.