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: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 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
  • Also Cited By: 3P33, 3P2X

  • 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 ...

    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: 
    • 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.,Sect.B 47: 127
    • Water structure in cubic insulin crystals
      Badager, J.,Caspar, D.L.
      (1991) Proc.Natl.Acad.Sci.USA 88: 622
    • Crystallographic titration of cubic insulin crystals: pH affects GluB13 switching and sulfate binding
      Diao, J.
      (2003) Acta Crystallogr.,Sect.D 59: 670
    • Structure of cubic insulin crystals in glucose solutions
      Yu, B.,Caspar, D.L.
      (1998) Biophys.J. 74: 616
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin
A, C
21Homo sapiensMutation(s): 1 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Insulin
B, D
30Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IPH
Query on IPH

Download SDF File 
Download CCD File 
A, C
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 70.852α = 90.00
b = 70.852β = 90.00
c = 70.852γ = 90.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
CNSrefinement
PROTEUM PLUSdata scaling
PROTEUM PLUSdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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