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PDBsum entry 1zk6

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protein links
Isomerase PDB id
1zk6
Jmol
Contents
Protein chain
91 a.a. *
* Residue conservation analysis
PDB id:
1zk6
Name: Isomerase
Title: Nmr solution structure of b. Subtilis prsa ppiase
Structure: Foldase protein prsa. Chain: a. Fragment: ppiase domain. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: prsa. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 15 models
Authors: H.Tossavainen,P.Permi,S.L.Purhonen,M.Sarvas,I.Kilpelainen, R.Seppala
Key ref:
H.Tossavainen et al. (2006). NMR solution structure and characterization of substrate binding site of the PPIase domain of PrsA protein from Bacillus subtilis. FEBS Lett, 580, 1822-1826. PubMed id: 16516208 DOI: 10.1016/j.febslet.2006.02.042
Date:
02-May-05     Release date:   28-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24327  (PRSA_BACSU) -  Foldase protein PrsA
Seq:
Struc:
292 a.a.
91 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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.febslet.2006.02.042 FEBS Lett 580:1822-1826 (2006)
PubMed id: 16516208  
 
 
NMR solution structure and characterization of substrate binding site of the PPIase domain of PrsA protein from Bacillus subtilis.
H.Tossavainen, P.Permi, S.L.Purhonen, M.Sarvas, I.Kilpeläinen, R.Seppala.
 
  ABSTRACT  
 
PrsA is a peptidyl-prolyl isomerase (PPIase) from Bacillus subtilis belonging to the parvulin family of PPIases. It is a membrane bound lipoprotein at the membrane-wall interface, involved in folding of exported proteins. We present the NMR solution structure of the PPIase domain of PrsA, the first from a Gram-positive bacterium. In addition we mapped out the active site with NMR titration experiments. A high degree of conservation with other members of the parvulin family was revealed in the structure and binding site. Interactions with substrate peptides were also characterized by mutated domains revealing that H122 is indispensable for overall correct folding.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Superimposition of PrsA-PPI (red) and the PPIase domain of hPin1 (blue, residues 54–163, PDB ID 1pin). Backbone atoms of secondary structures were used in the fit. Residues of the catalytic site are highlighted.
Figure 3.
Fig. 3. Characterization of the peptide binding site of PrsA-PPI. (A) Chemical shift changes observed upon binding of Suc-AKPF-pNA (black), Suc-AYPF-pNA (grey) and Suc-ANPF-pNA (blue). Changes at PrsA-PPI to peptide molar ratio 1:16 are shown. (B) Residues significantly perturbed upon binding are highlighted on PrsA-PPI structure. Red codes for large (0.07 slant Δδ < 0.36 ppm), and yellow for smaller (0.04 slant Δδ < 0.07 ppm) chemical shift changes. Backbone atoms of hPin1 (PDB ID 1pin) and PrsA-PPI were overlaid and the Ala-Pro dipeptide present in hPin1 structure is shown in blue. (C) A molecular surface representations of PrsA-PPI coloured according to its electrostatic potential. Negative residues are coloured in red, and positive in blue.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2006, 580, 1822-1826) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20623345 A.Kyburz, V.Raulinaitis, O.Koskela, V.Kontinen, P.Permi, I.Kilpelainen, and R.Seppala (2010).
1H, 13C and 15N resonance assignments of the major extracytoplasmic domain of the cell shape-determining protein MreC from Bacillus subtilis.
  Biomol NMR Assign, 4, 235-238.  
19451247 F.Alonzo, G.C.Port, M.Cao, and N.E.Freitag (2009).
The posttranslocation chaperone PrsA2 contributes to multiple facets of Listeria monocytogenes pathogenesis.
  Infect Immun, 77, 2612-2623.  
19309529 O.Heikkinen, R.Seppala, H.Tossavainen, S.Heikkinen, H.Koskela, P.Permi, and I.Kilpeläinen (2009).
Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA--implications for the catalytic mechanism of parvulins.
  BMC Struct Biol, 9, 17.
PDB code: 2jzv
  19787094 J.W.Mueller, and P.Bayer (2008).
Small family with key contacts: par14 and par17 parvulin proteins, relatives of pin1, now emerge in biomedical research.
  Perspect Medicin Chem, 2, 11-20.  
16632472 X.Kang, Y.Hu, Y.Li, X.Guo, X.Jiang, L.Lai, B.Xia, and C.Jin (2006).
Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases.
  J Biol Chem, 281, 18216-18226.
PDB code: 2f3i
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.