PDBsum entry 2ose

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Isomerase PDB id
Protein chain
195 a.a. *
_CL ×2
Waters ×77
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of the mimivirus cyclophilin
Structure: Probable peptidyl-prolyl cis-trans isomerase. Chain: a. Synonym: ppiase, rotamase. Engineered: yes
Source: Mimivirus. Organism_taxid: 315393. Gene: mimi_l605. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.04Å     R-factor:   0.216     R-free:   0.255
Authors: E.Z.Eisenmesser,V.Thai,P.Renesto,D.Raoult
Key ref:
V.Thai et al. (2008). Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus. J Mol Biol, 378, 71-86. PubMed id: 18342330 DOI: 10.1016/j.jmb.2007.08.051
05-Feb-07     Release date:   18-Dec-07    
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Protein chain
Pfam   ArchSchema ?
Q5UP71  (PPIL_MIMIV) -  Structural PPIase-like protein L605
234 a.a.
195 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     virion   2 terms 
  Biological process     protein folding   2 terms 
  Biochemical function     peptidyl-prolyl cis-trans isomerase activity     1 term  


DOI no: 10.1016/j.jmb.2007.08.051 J Mol Biol 378:71-86 (2008)
PubMed id: 18342330  
Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus.
V.Thai, P.Renesto, C.A.Fowler, D.J.Brown, T.Davis, W.Gu, D.D.Pollock, D.Kern, D.Raoult, E.Z.Eisenmesser.
Although multiple viruses utilize host cell cyclophilins, including severe acute respiratory syndrome (SARS) and human immunodeficiency virus type-1(HIV-1), their role in infection is poorly understood. To help elucidate these roles, we have characterized the first virally encoded cyclophilin (mimicyp) derived from the largest virus discovered to date (the Mimivirus) that is also a causative agent of pneumonia in humans. Mimicyp adopts a typical cyclophilin-fold, yet it also forms trimers unlike any previously characterized homologue. Strikingly, immunofluorescence assays reveal that mimicyp localizes to the surface of the mature virion, as recently proposed for several viruses that recruit host cell cyclophilins such as SARS and HIV-1. Additionally mimicyp lacks peptidyl-prolyl isomerase activity in contrast to human cyclophilins. Thus, this study suggests that cyclophilins, whether recruited from host cells (i.e. HIV-1 and SARS) or virally encoded (i.e. Mimivirus), are localized on viral surfaces for at least a subset of viruses.
  Selected figure(s)  
Figure 2.
Figure 2. Crystallographic interactions of mimicyp and comparison to hCypA interactions with the HIV-1 capsid. (a) MimiCyp crystallizes with four trimers within each unit cell. Each monomer within the trimer interacts via a basic loop insertion, residues 188–194 (KPYAGRK) into the putative active site of a neighboring monomer. Residues on the opposite side of the monomer from the putative active site, including residues within the C-terminal helix, mediate trimer–trimer contacts. (b) Close-up of the basic loop insertion into the acidic putative active site that forms each trimer. The basic loop is shown in green with heavy atoms of side-chains included and the active site is shown as a surface representation with basic residues shown in blue, acidic residues in red, and uncharged or hydrophobic residues in white. (c) Intermolecular electrostatic side-chain pairs that stabilize the trimer are formed between Lys188, Arg193, Lys194 from the basic loop and Asp164, Asp144 and Asp94 of the putative acidic active site, respectively. (d) Intermolecular electrostatic pairs that stabilize trimer–trimer formation include side-chain interactions of Asp178–Arg30 and Ser209–Lys34, and intermolecular hydrogen bonds formed between backbone carbonyl oxygen atoms of Tyr174 and Leu207 with the side-chains of Gln32 and Gln172, respectively. (e) Overlay of mimicyp intermolecular interactions with the hCypA/HIV-1 capsid complex (PDB accession number 1AK4) exhibits both similarities and differences. The mimicyp residues 188–194 are shown that comprise a type II β-turn, Tyr190–Arg193, and the HIV-1 capsid residues 483–494 form a relatively extended structure. These loops bind to each cyclophilin in opposing directions, yet approximately half of the residues within each, i.e. comprising the HIV-1 capsid loop and the neighboring mimicyp inserted loop, are nearly superimposed. The same secondary structural elements of mimicyp and hCypA shown in Figure 1 were used to align the two complexes.
Figure 7.
Figure 7. Self-association has been observed for several cyclophilins. Oligomeric interactions of (a) mimicyp, (b) human PPWD1-Cyp (PDB accession code 2A2N), (c) human cyclophilin-H (PDB accession code 1MZW), and (d) A. fumigatus cyclophilin (PDB accession code 2C3B) occur under concentrated protein conditions. For both PPWD1-Cyp and cyclophilin-H, only three monomers are shown yet these “end-to-end” interactions form a continuous array throughout the entire crystal lattice.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 378, 71-86) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20602248 A.Galat, and J.Bua (2010).
Molecular aspects of cyclophilins mediating therapeutic actions of their ligands.
  Cell Mol Life Sci, 67, 3467-3488.  
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
19403753 D.Byrne, R.Grzela, A.Lartigue, S.Audic, S.Chenivesse, S.Encinas, J.M.Claverie, and C.Abergel (2009).
The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'.
  Genome Res, 19, 1233-1242.  
19653859 J.M.Claverie, and C.Abergel (2009).
Mimivirus and its virophage.
  Annu Rev Genet, 43, 49-66.  
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