3B09

Crystal structure of the N-domain of FKBP22 from Shewanella sp. SIB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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Literature

Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: dimer dissociation by disruption of Val-Leu knot

Budiman, C.Angkawidjaja, C.Motoike, H.Koga, Y.Takano, K.Kanaya, S.

(2011) Protein Sci 20: 1755-1764

  • DOI: 10.1002/pro.714
  • Primary Citation of Related Structures:  
    3B09

  • PubMed Abstract: 
  • FK506-binding protein 22 (FKBP22) from the psychrotophic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) is a homodimeric protein with peptidyl prolyl cis-trans isomerase (PPIase) activity. Each monomer consists of the N-terminal domain responsible for dimerization and C-terminal catalytic domain ...

    FK506-binding protein 22 (FKBP22) from the psychrotophic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) is a homodimeric protein with peptidyl prolyl cis-trans isomerase (PPIase) activity. Each monomer consists of the N-terminal domain responsible for dimerization and C-terminal catalytic domain. To reveal interactions at the dimer interface of SIB1 FKBP22, the crystal structure of the N-domain of SIB1 FKBP22 (SN-FKBP22, residues 1-68) was determined at 1.9 Å resolution. SN-FKBP22 forms a dimer, in which each monomer consists of three helices (α1, α2, and α3N). In the dimer, two monomers have head-to-head interactions, in which residues 8-64 of one monomer form tight interface with the corresponding residues of the other. The interface is featured by the presence of a Val-Leu knot, in which Val37 and Leu41 of one monomer interact with Val41 and Leu37 of the other, respectively. To examine whether SIB1 FKBP22 is dissociated into the monomers by disruption of this knot, the mutant protein V37R/L41R-FKBP22, in which Val37 and Leu41 of SIB1 FKBP22 are simultaneously replaced by Arg, was constructed and biochemically characterized. This mutant protein was indistinguishable from the SIB1 FKBP22 derivative lacking the N-domain in oligomeric state, far-UV CD spectrum, thermal denaturation curve, PPIase activity, and binding ability to a folding intermediate of protein, suggesting that the N-domain of V37R/L41R-FKBP22 is disordered. We propose that a Val-Leu knot at the dimer interface of SIB1 FKBP22 is important for dimerization and dimerization is required for folding of the N-domain.


    Organizational Affiliation

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseA88Shewanella sp. SIB1Mutation(s): 0 
Gene Names: fklB
EC: 5.2.1.8
UniProt
Find proteins for Q765B0 (Shewanella sp. SIB1)
Explore Q765B0 
Go to UniProtKB:  Q765B0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ765B0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.703α = 90
b = 39.703β = 90
c = 101.6γ = 120
Software Package:
Software NamePurpose
BL44data collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release