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PDBsum entry 1xw7

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protein ligands metals Protein-protein interface(s) links
Hormone/growth factor PDB id
1xw7
Jmol PyMol
Contents
Protein chains
21 a.a.
30 a.a. *
Ligands
IPH ×2
Metals
_CL ×2
_ZN ×2
Waters ×80
* Residue conservation analysis
PDB id:
1xw7
Name: Hormone/growth factor
Title: Diabetes-associated mutations in human insulin: crystal stru photo-cross-linking studies of a-chain variant insulin waka
Structure: Insulin. Chain: a, c. Engineered: yes. Mutation: yes. Insulin. Chain: b, d. Engineered: yes
Source: Synthetic: yes. Other_details: the peptide was chemically synthesized. The of the peptide is naturally found in homo sapiens (human).. Of the peptide is naturally found in homo sapiens (human).
Biol. unit: Dodecamer (from PDB file)
Resolution:
2.30Å     R-factor:   0.205     R-free:   0.269
Authors: Z.L.Wan,K.Huang,B.Xu,Y.C.Chu,S.Q.Hu,P.G.Katsoyannis,M.A.Weis
Key ref:
Z.L.Wan et al. (2005). Diabetes-associated mutations in human insulin: crystal structure and photo-cross-linking studies of a-chain variant insulin Wakayama. Biochemistry, 44, 5000-5016. PubMed id: 15794638 DOI: 10.1021/bi047585k
Date:
29-Oct-04     Release date:   12-Apr-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
21 a.a.*
Protein chains
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
30 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biochemical function     hormone activity     1 term  

 

 
DOI no: 10.1021/bi047585k Biochemistry 44:5000-5016 (2005)
PubMed id: 15794638  
 
 
Diabetes-associated mutations in human insulin: crystal structure and photo-cross-linking studies of a-chain variant insulin Wakayama.
Z.L.Wan, K.Huang, B.Xu, S.Q.Hu, S.Wang, Y.C.Chu, P.G.Katsoyannis, M.A.Weiss.
 
  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. 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20333376 L.Wan, J.B.Chen, H.H.Chen, J.Huang, H.M.Yu, S.F.Luo, F.J.Tsai, and T.W.Chang (2010).
Genetic variations in the C epsilon mX domain of human membrane-bound IgE.
  Immunogenetics, 62, 273-280.  
19321435 B.Xu, K.Huang, Y.C.Chu, S.Q.Hu, S.Nakagawa, S.Wang, R.Y.Wang, J.Whittaker, P.G.Katsoyannis, and M.A.Weiss (2009).
Decoding the Cryptic Active Conformation of a Protein by Synthetic Photoscanning: INSULIN INSERTS A DETACHABLE ARM BETWEEN RECEPTOR DOMAINS.
  J Biol Chem, 284, 14597-14608.  
19139090 C.L.Alvino, K.A.McNeil, S.C.Ong, C.Delaine, G.W.Booker, J.C.Wallace, J.Whittaker, and B.E.Forbes (2009).
A Novel Approach to Identify Two Distinct Receptor Binding Surfaces of Insulin-like Growth Factor II.
  J Biol Chem, 284, 7656-7664.  
19274663 C.W.Ward, and M.C.Lawrence (2009).
Ligand-induced activation of the insulin receptor: a multi-step process involving structural changes in both the ligand and the receptor.
  Bioessays, 31, 422-434.  
19618407 G.Le Flem, J.Pecher, V.Le Flem-Bonhomme, A.Withdrawn, J.Rochette, J.P.Pujol, and P.Bogdanowicz (2009).
Human insulin A-chain peptide analog(s) with in vitro biological activity.
  Cell Biochem Funct, 27, 370-377.  
19773552 M.Zhao, Z.L.Wan, L.Whittaker, B.Xu, N.B.Phillips, P.G.Katsoyannis, F.Ismail-Beigi, J.Whittaker, and M.A.Weiss (2009).
Design of an insulin analog with enhanced receptor binding selectivity: rationale, structure, and therapeutic implications.
  J Biol Chem, 284, 32178-32187.
PDB code: 3fq9
19321436 Q.X.Hua, B.Xu, K.Huang, S.Q.Hu, S.Nakagawa, W.Jia, S.Wang, J.Whittaker, P.G.Katsoyannis, and M.A.Weiss (2009).
Enhancing the Activity of a Protein by Stereospecific Unfolding: CONFORMATIONAL LIFE CYCLE OF INSULIN AND ITS EVOLUTIONARY ORIGINS.
  J Biol Chem, 284, 14586-14596.
PDB codes: 2k91 2k9r
18048361 L.Gauguin, B.Klaproth, W.Sajid, A.S.Andersen, K.A.McNeil, B.E.Forbes, and P.De Meyts (2008).
Structural Basis for the Lower Affinity of the Insulin-like Growth Factors for the Insulin Receptor.
  J Biol Chem, 283, 2604-2613.  
18989367 M.E.Rentería, N.S.Gandhi, P.Vinuesa, E.Helmerhorst, and R.L.Mancera (2008).
A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information.
  PLoS ONE, 3, e3667.  
18332129 Q.X.Hua, S.H.Nakagawa, W.Jia, K.Huang, N.B.Phillips, S.Q.Hu, and M.A.Weiss (2008).
Design of an active ultrastable single-chain insulin analog: synthesis, structure, and therapeutic implications.
  J Biol Chem, 283, 14703-14716.
PDB codes: 2jzq 3bxq
17475626 C.Delaine, C.L.Alvino, K.A.McNeil, T.D.Mulhern, L.Gauguin, P.De Meyts, E.Y.Jones, J.Brown, J.C.Wallace, and B.E.Forbes (2007).
A novel binding site for the human insulin-like growth factor-II (IGF-II)/mannose 6-phosphate receptor on IGF-II.
  J Biol Chem, 282, 18886-18894.  
17280834 C.W.Ward, M.C.Lawrence, V.A.Streltsov, T.E.Adams, and N.M.McKern (2007).
The insulin and EGF receptor structures: new insights into ligand-induced receptor activation.
  Trends Biochem Sci, 32, 129-137.  
17884811 K.Huang, S.J.Chan, Q.X.Hua, Y.C.Chu, R.Y.Wang, B.Klaproth, W.Jia, J.Whittaker, P.De Meyts, S.H.Nakagawa, D.F.Steiner, P.G.Katsoyannis, and M.A.Weiss (2007).
The A-chain of insulin contacts the insert domain of the insulin receptor. Photo-cross-linking and mutagenesis of a diabetes-related crevice.
  J Biol Chem, 282, 35337-35349.
PDB codes: 2jum 2juu 2juv
17851071 M.C.Lawrence, N.M.McKern, and C.W.Ward (2007).
Insulin receptor structure and its implications for the IGF-1 receptor.
  Curr Opin Struct Biol, 17, 699-705.  
17339314 S.J.Chan, S.Nakagawa, and D.F.Steiner (2007).
Complementation analysis demonstrates that insulin cross-links both alpha subunits in a truncated insulin receptor dimer.
  J Biol Chem, 282, 13754-13758.  
16894147 M.Lou, T.P.Garrett, N.M.McKern, P.A.Hoyne, V.C.Epa, J.D.Bentley, G.O.Lovrecz, L.J.Cosgrove, M.J.Frenkel, and C.W.Ward (2006).
The first three domains of the insulin receptor differ structurally from the insulin-like growth factor 1 receptor in the regions governing ligand specificity.
  Proc Natl Acad Sci U S A, 103, 12429-12434.
PDB code: 2hr7
16728398 Q.X.Hua, M.Liu, S.Q.Hu, W.Jia, P.Arvan, and M.A.Weiss (2006).
A conserved histidine in insulin is required for the foldability of human proinsulin: structure and function of an ALAB5 analog.
  J Biol Chem, 281, 24889-24899.
PDB code: 2h67
16762918 Q.X.Hua, S.Nakagawa, S.Q.Hu, W.Jia, S.Wang, and M.A.Weiss (2006).
Toward the active conformation of insulin: stereospecific modulation of a structural switch in the B chain.
  J Biol Chem, 281, 24900-24909.
PDB codes: 2hh4 2hho
16751187 S.H.Nakagawa, Q.X.Hua, S.Q.Hu, W.Jia, S.Wang, P.G.Katsoyannis, and M.A.Weiss (2006).
Chiral mutagenesis of insulin. Contribution of the B20-B23 beta-turn to activity and stability.
  J Biol Chem, 281, 22386-22396.  
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 code is shown on the right.

 

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