PDBsum entry 1xwn

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Isomerase PDB id
Jmol PyMol
Protein chain
166 a.a. *
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Solution structure of cyclophilin like 1(ppil1) and insights into its interaction with skip
Structure: Peptidyl-prolyl cis-trans isomerase like 1. Chain: a. Synonym: ppiase, rotamase, cgi-124, unq2425/pro4984. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ppil1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: C.Xu,Y.Xu,Y.Tang,J.Wu,Y.Shi,Q.Huang,Q.Zhang
Key ref:
C.Xu et al. (2006). Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP. J Biol Chem, 281, 15900-15908. PubMed id: 16595688 DOI: 10.1074/jbc.M511155200
01-Nov-04     Release date:   18-Oct-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9Y3C6  (PPIL1_HUMAN) -  Peptidyl-prolyl cis-trans isomerase-like 1
166 a.a.
166 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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!
  Cellular component     catalytic step 2 spliceosome   4 terms 
  Biological process     protein folding   5 terms 
  Biochemical function     protein binding     3 terms  


    Added reference    
DOI no: 10.1074/jbc.M511155200 J Biol Chem 281:15900-15908 (2006)
PubMed id: 16595688  
Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP.
C.Xu, J.Zhang, X.Huang, J.Sun, Y.Xu, Y.Tang, J.Wu, Y.Shi, Q.Huang, Q.Zhang.
The human PPIL1 (peptidyl prolyl isomerase-like protein 1) is a specific component of human 35 S U5 small nuclear ribonucleoprotein particle and 45 S activated spliceosome. It is recruited by SKIP, another essential component of 45 S activated spliceosome, into spliceosome just before the catalytic step 1. It stably associates with SKIP, which also exists in 35 S and activated spliceosome as a nuclear matrix protein. We report here the solution structure of PPIL1 determined by NMR spectroscopy. The structure of PPIL1 resembles other members of the cyclophilin family and exhibits PPIase activity. To investigate its interaction with SKIP in vitro, we identified the SKIP contact region by GST pulldown experiments and surface plasmon resonance. We provide direct evidence of PPIL1 stably associated with SKIP. The dissociation constant is 1.25 x 10(-7) M for the N-terminal peptide of SKIP-(59-129) with PPIL1. We also used chemical shift perturbation experiments to show the possible SKIP binding interface on PPIL1. These results illustrated that a novel cyclophilin-protein contact mode exists in the PPIL1-SKIP complex during activation of the spliceosome. The biological implication of this binding with spliceosome rearrangement during activation is discussed.
  Selected figure(s)  
Figure 3.
FIGURE 3. Structural feature of PPIL1. A, overlay of the structures of human PPIL1 (green) and human cyclophilin A (red). B, comparison between cyclosporin A binding sites of PPIL1 (colored as in panel A) and counterpart of cyclophilin A (white). Several secondary structure segments ( 3, 4, 5, 6) are shown for clarity. The orientation is the same as shown in Fig. 2. Four conserved residues of PPIL1 are superimposed upon the counterparts of cyclophilin A, which are colored red and green, respectively. The atoms of the key residues involved in formation of intermolecular bonds in the cyclophilin-Cyclosporin complex are labeled in blue.
Figure 4.
FIGURE 4. Sequence alignments. Sequence alignments of PPIL1 with cyclophilin A from Homo sapiens, accession code NP_066953 (CYPA_HUMAN); cyclophilin B from H. sapiens, accession code NP_000933 (CYPB_HUMAN); cyclophilin C from H. sapiens, accession code NP_000934; SnuCyp-20 from H. sapiens, accession code NP_006338 (CYPH_HUMAN). The sequences were aligned by CLUSTAL_W with dashes introduced for maximum alignment. Conserved residues involved in binding inhibitors and substrates in Cyp A were labeled with stars.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 15900-15908) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20368803 C.M.Stegmann, R.Lührmann, and M.C.Wahl (2010).
The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein.
  PLoS One, 5, e10013.
PDB code: 2x7k
20676357 T.L.Davis, J.R.Walker, V.Campagna-Slater, P.J.Finerty, R.Paramanathan, G.Bernstein, F.MacKenzie, W.Tempel, H.Ouyang, W.H.Lee, E.Z.Eisenmesser, and S.Dhe-Paganon (2010).
Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
  PLoS Biol, 8, e1000439.  
19555495 J.Krücken, G.Greif, and G.von Samson-Himmelstjerna (2009).
In silico analysis of the cyclophilin repertoire of apicomplexan parasites.
  Parasit Vectors, 2, 27.  
19883504 L.Van Landeghem, M.M.Mahé, R.Teusan, J.Léger, I.Guisle, R.Houlgatte, and M.Neunlist (2009).
Regulation of intestinal epithelial cells transcriptome by enteric glial cells: impact on intestinal epithelial barrier functions.
  BMC Genomics, 10, 507.  
18854154 R.König, Y.Zhou, D.Elleder, T.L.Diamond, G.M.Bonamy, J.T.Irelan, C.Y.Chiang, B.P.Tu, P.D.De Jesus, C.E.Lilley, S.Seidel, A.M.Opaluch, J.S.Caldwell, M.D.Weitzman, K.L.Kuhen, S.Bandyopadhyay, T.Ideker, A.P.Orth, L.J.Miraglia, F.D.Bushman, J.A.Young, and S.K.Chanda (2008).
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication.
  Cell, 135, 49-60.  
18397323 T.L.Davis, J.R.Walker, H.Ouyang, F.MacKenzie, C.Butler-Cole, E.M.Newman, E.Z.Eisenmesser, and S.Dhe-Paganon (2008).
The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1).
  FEBS J, 275, 2283-2295.
PDB code: 2a2n
18074396 R.L.Rich, and D.G.Myszka (2007).
Survey of the year 2006 commercial optical biosensor literature.
  J Mol Recognit, 20, 300-366.  
17763922 Y.Shi, and J.Wu (2007).
Structural basis of protein-protein interaction studied by NMR.
  J Struct Funct Genomics, 8, 67-72.  
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.