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PDBsum entry 2pv3

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
2pv3
Jmol
Contents
Protein chains
284 a.a. *
Ligands
ASN-PHE-THR-LEU-
LYS-PHE-TRP-ASP-
ILE-PHE
* Residue conservation analysis
PDB id:
2pv3
Name: Isomerase
Title: Crystallographic structure of sura fragment lacking the seco peptidyl-prolyl isomerase domain complexed with peptide nft
Structure: Chaperone sura. Chain: a, b. Fragment: survivial protein a fragment from which the secon peptidyl-prolyl isomerase domain has been deleted. Synonym: peptidyl-prolyl cis-trans isomerase sura, ppiase s rotamase sura, survival protein a. Engineered: yes. C-peptide. Chain: c.
Source: Escherichia coli. Organism_taxid: 562. Strain: k-12 emg2. Gene: sura. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes
Resolution:
3.39Å     R-factor:   0.284     R-free:   0.299
Authors: X.Xu,D.B.Mckay
Key ref:
X.Xu et al. (2007). The periplasmic bacterial molecular chaperone SurA adapts its structure to bind peptides in different conformations to assert a sequence preference for aromatic residues. J Mol Biol, 373, 367-381. PubMed id: 17825319 DOI: 10.1016/j.jmb.2007.07.069
Date:
09-May-07     Release date:   02-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ABZ6  (SURA_ECOLI) -  Chaperone SurA
Seq:
Struc:
428 a.a.
284 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 33 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     isomerase activity     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.jmb.2007.07.069 J Mol Biol 373:367-381 (2007)
PubMed id: 17825319  
 
 
The periplasmic bacterial molecular chaperone SurA adapts its structure to bind peptides in different conformations to assert a sequence preference for aromatic residues.
X.Xu, S.Wang, Y.X.Hu, D.B.McKay.
 
  ABSTRACT  
 
The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity. The peptide recognition is imparted by the first peptidyl-prolyl isomerase (PPIase) domain of SurA. Crystal structures of complexes between peptides of sequence WEYIPNV and NFTLKFWDIFRK with the first PPIase domain of the Escherichia coli SurA protein at 1.3 A resolution, and of a complex between the dodecapeptide and a SurA fragment lacking the second PPIase domain at 3.4 A resolution, have been solved. SurA binds as a monomer to the heptapeptide in an extended conformation. It binds as a dimer to the dodecapeptide in an alpha-helical conformation, predicated on a substantial structural rearrangement of the SurA protein. In both cases, side-chains of aromatic residues of the peptides contribute a large fraction of the binding interactions. SurA therefore asserts a recognition preference for aromatic amino acids in a variety of sequence configurations by adopting alternative tertiary and quaternary structures to bind peptides in different conformations.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Views of the complex of the C-peptide with SurA-P1. (a) Ribbon drawing of the complex. (b) View showing interactions of peptide with subunit A of SurA-P1 dimer. (c) View showing interactions of peptide with subunit B of SurA-P1 dimer. Colors are the same as for Figure 3.
Figure 5.
Figure 5. Space-filling views of the complex of the C-peptide with individual subunits of SurA-P1. (a) View of complex between peptide and subunit A of SurA-P1 dimer. (b) View of complex between peptide and subunit B of SurA-P1 dimer. Colors are the same as for Figure 3.
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 373, 367-381) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20378773 C.L.Hagan, S.Kim, and D.Kahne (2010).
Reconstitution of outer membrane protein assembly from purified components.
  Science, 328, 890-892.  
  19866485 U.Weininger, R.P.Jakob, M.Kovermann, J.Balbach, and F.X.Schmid (2010).
The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity.
  Protein Sci, 19, 6.
PDB code: 2kgj
20515934 Y.T.Yen, C.Tsang, T.A.Cameron, D.O.Ankrah, A.Rodou, and C.Stathopoulos (2010).
Importance of conserved residues of the serine protease autotransporter beta-domain in passenger domain processing and beta-barrel assembly.
  Infect Immun, 78, 3516-3528.  
19399587 D.M.Walther, D.Rapaport, and J.Tommassen (2009).
Biogenesis of beta-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence.
  Cell Mol Life Sci, 66, 2789-2804.  
19734313 F.Ruiz-Perez, I.R.Henderson, D.L.Leyton, A.E.Rossiter, Y.Zhang, and J.P.Nataro (2009).
Roles of periplasmic chaperone proteins in the biogenesis of serine protease autotransporters of Enterobacteriaceae.
  J Bacteriol, 191, 6571-6583.  
19181847 T.A.Walton, C.M.Sandoval, C.A.Fowler, A.Pardi, and M.C.Sousa (2009).
The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains.
  Proc Natl Acad Sci U S A, 106, 1772-1777.  
  18765910 A.Wohlkönig, H.Hodak, B.Clantin, M.Sénéchal, C.Bompard, F.Jacob-Dubuisson, and V.Villeret (2008).
Crystallization and preliminary X-ray diffraction analysis of the peptidylprolyl isomerase Par27 of Bordetella pertussis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 809-812.  
18498364 K.H.Stymest, and P.Klappa (2008).
The periplasmic peptidyl prolyl cis-trans isomerases PpiD and SurA have partially overlapping substrate specificities.
  FEBS J, 275, 3470-3479.  
18836534 K.M.Watts, and D.A.Hunstad (2008).
Components of SurA required for outer membrane biogenesis in uropathogenic Escherichia coli.
  PLoS ONE, 3, e3359.  
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.