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PDBsum entry 3kl4
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protein Protein-protein interface(s) links
Hydrolase PDB id
3kl4

 

 

 

 

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Contents
Protein chains
413 a.a. *
21 a.a. *
* Residue conservation analysis
PDB id:
3kl4
Name: Hydrolase
Title: Recognition of a signal peptide by the signal recognition particle
Structure: Signal recognition 54 kda protein. Chain: a. Fragment: unp residues 2-432. Synonym: srp54. Engineered: yes. Signal peptide of yeast dipeptidyl aminopeptidase b. Chain: b. Fragment: unp residues 26-51. Synonym: dpap b, yscv.
Source: Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Gene: srp54, sso0971. Expressed in: escherichia coli. Expression_system_taxid: 562. Saccharomyces cerevisiae. Organism_taxid: 4932.
Resolution:
3.50Å     R-factor:   0.301     R-free:   0.322
Authors: C.Y.Janda,K.Nagai,J.Li,C.Oubridge
Key ref: C.Y.Janda et al. (2010). Recognition of a signal peptide by the signal recognition particle. Nature, 465, 507-510. PubMed id: 20364120
Date:
06-Nov-09     Release date:   31-Mar-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q97ZE7  (SRP54_SULSO) -  Signal recognition particle 54 kDa protein from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		447 a.a.
413 a.a.*
Protein chain
Pfam   ArchSchema ?
P18962  (DAP2_YEAST) -  Dipeptidyl aminopeptidase B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		818 a.a.
21 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: Chain A: E.C.3.6.5.4  - signal-recognition-particle GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate + H+
GTP
 + H2O
 = GDP
 + phosphate
 + H(+)
   Enzyme class 2: Chain B: E.C.3.4.14.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Nature 465:507-510 (2010)
PubMed id: 20364120  
 
 
Recognition of a signal peptide by the signal recognition particle.
C.Y.Janda, J.Li, C.Oubridge, H.Hernández, C.V.Robinson, K.Nagai.
 
  ABSTRACT  
 
Targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (SRP) when nascent polypeptide chains emerge from the ribosome. The SRP-ribosome nascent chain complex is then targeted through its GTP-dependent interaction with SRP receptor to the protein-conducting channel on endoplasmic reticulum membrane in eukaryotes or plasma membrane in bacteria. A universally conserved component of SRP (refs 1, 2), SRP54 or its bacterial homologue, fifty-four homologue (Ffh), binds the signal peptides, which have a highly divergent sequence divisible into a positively charged n-region, an h-region commonly containing 8-20 hydrophobic residues and a polar c-region. No structure has been reported that exemplifies SRP54 binding of any signal sequence. Here we have produced a fusion protein between Sulfolobus solfataricus SRP54 (Ffh) and a signal peptide connected via a flexible linker. This fusion protein oligomerizes in solution through interaction between the SRP54 and signal peptide moieties belonging to different chains, and it is functional, as demonstrated by its ability to bind SRP RNA and SRP receptor FtsY. We present the crystal structure at 3.5 A resolution of an SRP54-signal peptide complex in the dimer, which reveals how a signal sequence is recognized by SRP54.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23235881 K.Shen, S.Arslan, D.Akopian, T.Ha, and S.O.Shan (2012).
Activated GTPase movement on an RNA scaffold drives co-translational protein targeting.
  Nature, 492, 271-275.  
23142984 W.Holtkamp, S.Lee, T.Bornemann, T.Senyushkina, M.V.Rodnina, and W.Wintermeyer (2012).
Dynamic switch of the signal recognition particle from scanning to targeting.
  Nat Struct Mol Biol, 19, 1332-1337.  
  21291501 I.Saraogi, and S.O.Shan (2011).
Molecular mechanism of co-translational protein targeting by the signal recognition particle.
  Traffic, 12, 535-542.  
21341830 P.Varilly, A.J.Patel, and D.Chandler (2011).
An improved coarse-grained model of solvation and the hydrophobic effect.
  J Chem Phys, 134, 074109.  
22086371 R.S.Hegde, and R.J.Keenan (2011).
Tail-anchored membrane protein insertion into the endoplasmic reticulum.
  Nat Rev Mol Cell Biol, 12, 787-798.  
21330537 S.F.Ataide, N.Schmitz, K.Shen, A.Ke, S.O.Shan, J.A.Doudna, and N.Ban (2011).
The crystal structure of the signal recognition particle in complex with its receptor.
  Science, 331, 881-886.
PDB code: 2xxa
21336278 T.Hainzl, S.Huang, G.Meriläinen, K.Brännström, and A.E.Sauer-Eriksson (2011).
Structural basis of signal-sequence recognition by the signal recognition particle.
  Nat Struct Mol Biol, 18, 389-391.
PDB code: 3ndb
  20672053 C.Zwieb, and S.Bhuiyan (2010).
Archaea signal recognition particle shows the way.
  Archaea, 2010, 485051.  
20850366 F.Wang, E.C.Brown, G.Mak, J.Zhuang, and V.Denic (2010).
A chaperone cascade sorts proteins for posttranslational membrane insertion into the endoplasmic reticulum.
  Mol Cell, 40, 159-171.  
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.

 

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