1XW7

Diabetes-Associated Mutations in Human Insulin: Crystal Structure and Photo-Cross-Linking Studies of A-Chain Variant Insulin Wakayama


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Diabetes-associated mutations in human insulin: crystal structure and photo-cross-linking studies of a-chain variant insulin wakayama

Wan, Z.L.Huang, K.Xu, B.Hu, S.Q.Wang, S.Chu, Y.C.Katsoyannis, P.G.Weiss, M.A.

(2005) Biochemistry 44: 5000-5016

  • DOI: 10.1021/bi047585k
  • Primary Citation of Related Structures:  
    1XW7

  • PubMed Abstract: 
  • Naturally occurring mutations in insulin associated with diabetes mellitus identify critical determinants of its biological activity. Here, we describe the crystal structure of insulin Wakayama, a clinical variant in which a conserved valine in the A chain (residue A3) is substituted by leucine ...

    Naturally occurring mutations in insulin associated with diabetes mellitus identify critical determinants of its biological activity. Here, we describe the crystal structure of insulin Wakayama, a clinical variant in which a conserved valine in the A chain (residue A3) is substituted by leucine. The substitution occurs within a crevice adjoining the classical receptor-binding surface and impairs receptor binding by 500-fold, an unusually severe decrement among mutant insulins. To resolve whether such decreased activity is directly or indirectly mediated by the variant side chain, we have determined the crystal structure of Leu(A3)-insulin and investigated the photo-cross-linking properties of an A3 analogue containing p-azidophenylalanine. The structure, characterized in a novel crystal form as an R(6) zinc hexamer at 2.3 A resolution, is essentially identical to that of the wild-type R(6) hexamer. The variant side chain remains buried in a nativelike crevice with small adjustments in surrounding side chains. The corresponding photoactivatable analogue, although of low affinity, exhibits efficient cross-linking to the insulin receptor. The site of photo-cross-linking lies within a 14 kDa C-terminal domain of the alpha-subunit. This domain, unrelated in sequence to the major insulin-binding region in the N-terminal L1 beta-helix, is also contacted by photoactivatable probes at positions A8 and B25. Packing of Val(A3) at this interface may require a conformational change in the B chain to expose the A3-related crevice. The structure of insulin Wakayama thus evokes the reasoning of Sherlock Holmes in "the curious incident of the dog in the night": the apparent absence of structural perturbations (like the dog that did not bark) provides a critical clue to the function of a hidden receptor-binding surface.


    Related Citations: 
    • Crystallographic titration of cubic insulin crystals: pH affects GluB13 switching and sulfate binding
      Diao, J.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 670
    • Structure of cubic insulin crystals in glucose solutions
      Yu, B., Caspar, D.L.
      (1998) Biophys J 74: 616
    • Structure of the pig insulin dimer in the cubic crystal
      Badger, J., Harris, M.R., Reynolds, C.D., Evans, A.C., Dodson, E.J., Dodson, G.G., North, A.C.
      (1991) Acta Crystallogr B 47: 127
    • Water structure in cubic insulin crystals
      Badager, J., Caspar, D.L.
      (1991) Proc Natl Acad Sci U S A 88: 622
    • Zinc-free cubic pig insulin: crystallization and structure determination
      Dodson, E.J., Dodson, G.G., Lewitova, A., Sabesan, M.
      (1978) J Mol Biol 125: 387

    Organizational Affiliation

    Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4935, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin AC21N/AMutation(s): 1 
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS:  P01308
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin BD30N/AMutation(s): 0 
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS:  P01308
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.852α = 90
b = 70.852β = 90
c = 70.852γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
CNSrefinement
PROTEUM PLUSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description