PDBsum entry 1ix5

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protein links
Isomerase PDB id
Jmol PyMol
Protein chain
151 a.a. *
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Solution structure of the methanococcus thermolithotrophicus fkbp
Structure: Fkbp. Chain: a. Synonym: fkbp-type peptidyl-prolyl cis-trans isomerase. Engineered: yes. Mutation: yes
Source: Methanothermococcus thermolithotrophicus. Organism_taxid: 2186. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 10 models
Authors: R.Suzuki,K.Nagata,M.Kawakami,N.Nemoto,M.Furutani,K.Adachi, T.Maruyama,M.Tanokura
Key ref:
R.Suzuki et al. (2003). Three-dimensional solution structure of an archaeal FKBP with a dual function of peptidyl prolyl cis-trans isomerase and chaperone-like activities. J Mol Biol, 328, 1149-1160. PubMed id: 12729748 DOI: 10.1016/S0022-2836(03)00379-6
12-Jun-02     Release date:   10-Jun-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O52980  (FKBP_METTL) -  FKBP-type peptidyl-prolyl cis-trans isomerase
154 a.a.
151 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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!
  Biological process     protein peptidyl-prolyl isomerization   1 term 
  Biochemical function     isomerase activity     2 terms  


    Added reference    
DOI no: 10.1016/S0022-2836(03)00379-6 J Mol Biol 328:1149-1160 (2003)
PubMed id: 12729748  
Three-dimensional solution structure of an archaeal FKBP with a dual function of peptidyl prolyl cis-trans isomerase and chaperone-like activities.
R.Suzuki, K.Nagata, F.Yumoto, M.Kawakami, N.Nemoto, M.Furutani, K.Adachi, T.Maruyama, M.Tanokura.
Here we report the solution structure of an archaeal FK506-binding protein (FKBP) from a thermophilic archaeum, Methanococcus thermolithotrophicus (MtFKBP17), which has peptidyl prolyl cis-trans isomerase (PPIase) and chaperone-like activities, to reveal the structural basis for the dual function. In addition to a typical PPIase domain, a newly identified domain is formed in the flap loop by a 48-residue insert that is required for the chaperone-like activity. The new domain, called IF domain (the Insert in the Flap), is a novel-folding motif and exposes a hydrophobic surface, which we consider to play an important role in the chaperone-like activity.
  Selected figure(s)  
Figure 4.
Figure 4. Overlay of the solution structure of MtFKBP17 and the crystal structure of HsFKBP12. The C^a atoms used for superimposition are colored red and blue, while the other C^a atoms are colored pink and light blue in MtFKBP17 and HsFKBP12, respectively.
Figure 8.
Figure 8. Hydrophobic surface of the IF domain of MtFKBP17. Amino acid residues forming the hydrophobic surface are shown and labeled.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 1149-1160) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20306145 T.Unger, O.Dym, S.Albeck, Y.Jacobovitch, R.Bernehim, D.Marom, O.Pisanty, and A.Breiman (2010).
Crystal structure of the three FK506 binding protein domains of wheat FKBP73: evidence for a unique wFK73_2 domain.
  J Struct Funct Genomics, 11, 113-123.
PDB codes: 3jxv 3jym
19558490 C.Budiman, K.Bando, C.Angkawidjaja, Y.Koga, K.Takano, and S.Kanaya (2009).
Engineering of monomeric FK506-binding protein 22 with peptidyl prolyl cis-trans isomerase. Importance of a V-shaped dimeric structure for binding to protein substrate.
  FEBS J, 276, 4091-4101.  
19645725 L.Martino, Y.He, K.L.Hands-Taylor, E.R.Valentine, G.Kelly, C.Giancola, and M.R.Conte (2009).
The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity.
  FEBS J, 276, 4529-4544.
PDB code: 2kfw
18214965 J.A.Somarelli, S.Y.Lee, J.Skolnick, and R.J.Herrera (2008).
Structure-based classification of 45 FK506-binding proteins.
  Proteins, 72, 197-208.  
18065652 J.Stie, and D.Fox (2008).
Calcineurin regulation in fungi and beyond.
  Eukaryot Cell, 7, 177-186.  
17720786 J.W.Zhang, M.R.Leach, and D.B.Zamble (2007).
The peptidyl-prolyl isomerase activity of SlyD is not required for maturation of Escherichia coli hydrogenase.
  J Bacteriol, 189, 7942-7944.  
17426034 M.R.Leach, J.W.Zhang, and D.B.Zamble (2007).
The role of complex formation between the Escherichia coli hydrogenase accessory factors HypB and SlyD.
  J Biol Chem, 282, 16177-16186.  
15569666 J.W.Zhang, G.Butland, J.F.Greenblatt, A.Emili, and D.B.Zamble (2005).
A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway.
  J Biol Chem, 280, 4360-4366.  
15687202 R.Kern, A.Malki, J.Abdallah, J.C.Liebart, C.Dubucs, M.H.Yu, and G.Richarme (2005).
Protein isoaspartate methyltransferase is a multicopy suppressor of protein aggregation in Escherichia coli.
  J Bacteriol, 187, 1377-1383.  
15356344 G.Gopalan, Z.He, Y.Balmer, P.Romano, R.Gupta, A.Héroux, B.B.Buchanan, K.Swaminathan, and S.Luan (2004).
Structural analysis uncovers a role for redox in regulating FKBP13, an immunophilin of the chloroplast thylakoid lumen.
  Proc Natl Acad Sci U S A, 101, 13945-13950.
PDB code: 1u79
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 codes are shown on the right.