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PDBsum entry 3bao

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protein ligands Protein-protein interface(s) links
Hormone PDB id
3bao
Jmol
Contents
Protein chains
141 a.a. *
Ligands
SO4
FMT ×4
Waters ×224
* Residue conservation analysis
PDB id:
3bao
Name: Hormone
Title: Crystal structure of l26n mutant of human acidic fibroblast growth factor
Structure: Heparin-binding growth factor 1. Chain: a, b. Synonym: hbgf-1, acidic fibroblast growth factor, afgf, beta-endothelial cell growth factor, ecgf-beta. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: fgf1, fgfa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.55Å     R-factor:   0.194     R-free:   0.211
Authors: J.Lee,M.Blaber
Key ref:
J.Lee et al. (2008). A logical OR redundancy within the Asx-Pro-Asx-Gly type I beta-turn motif. J Mol Biol, 377, 1251-1264. PubMed id: 18308335 DOI: 10.1016/j.jmb.2008.01.055
Date:
08-Nov-07     Release date:   15-Apr-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05230  (FGF1_HUMAN) -  Fibroblast growth factor 1
Seq:
Struc:
155 a.a.
141 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   8 terms 
  Biological process     Fc-epsilon receptor signaling pathway   26 terms 
  Biochemical function     S100 protein binding     7 terms  

 

 
DOI no: 10.1016/j.jmb.2008.01.055 J Mol Biol 377:1251-1264 (2008)
PubMed id: 18308335  
 
 
A logical OR redundancy within the Asx-Pro-Asx-Gly type I beta-turn motif.
J.Lee, V.K.Dubey, L.M.Longo, M.Blaber.
 
  ABSTRACT  
 
Turn secondary structure is essential to the formation of globular protein architecture. Turn structures are, however, much more complex than either alpha-helix or beta-sheet, and the thermodynamics and folding kinetics are poorly understood. Type I beta-turns are the most common type of reverse turn, and they exhibit a statistical consensus sequence of Asx-Pro-Asx-Gly (where Asx is Asp or Asn). A comprehensive series of individual and combined Asx mutations has been constructed within three separate type I 3:5 G1 bulge beta-turns in human fibroblast growth factor-1, and their effects on structure, stability, and folding have been determined. The results show a fundamental logical OR relationship between the Asx residues in the motif, involving H-bond interactions with main-chain amides within the turn. These interactions can be modulated by additional interactions with residues adjacent to the turn at positions i+4 and i+6. The results show that the Asx residues in the turn motif make a substantial contribution to the overall stability of the protein, and the Asx logical OR relationship defines a redundant system that can compensate for deleterious point mutations. The results also show that the stability of the turn is unlikely to be the prime determinant of formation of turn structure in the folding transition state.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. (a) Overlay of mutant X-ray structures NPAG (turn 2), DPAG (turn 2), DTAG (turn 6), and NKAG (turn 10) mutant structures. These structures evaluate the orientation of Asx at position i when position i + 2 is Ala. With the exception of the NPAG structure, in each case, the Asx at position i adopts a gauche^− rotamer and H-bonds with the main-chain amide of turn residues i + 2 and i + 4. The Asn in the NPAG structure adopts a gauche^+ rotamer and H-bonds with the i + 6 Asp side chain. (b) Overlay of mutant X-ray structures APDG (turn 2), APNG (turn 2), KKNG (turn 10), and WT turn 2 structure LPDG. These structures evaluate the orientation of Asx at position i + 2 when position i is Ala (or non-Asx as in the KKNG and LPDG structures). In each case, the Asx at position i + 2 adopts a gauche^− rotamer and H-bonds with the main-chain amide of turn residue i + 4. The solvent provides the H-bond partner for the main-chain amide at the turn position i + 2.
Figure 8.
Fig. 8. Thermodynamic cycle for Ala mutations in the WT FGF-1 turn 6 (DTDG) structure that illustrates the logical OR relationship of the Asx residues that provides for redundancy in stability.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 377, 1251-1264) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21173271 J.Lee, and M.Blaber (2011).
Experimental support for the evolution of symmetric protein architecture from a simple peptide motif.
  Proc Natl Acad Sci U S A, 108, 126-130.
PDB codes: 3o49 3o4a 3o4b 3o4c 3o4d 3ogf 3ol0
21315087 J.Lee, S.I.Blaber, V.K.Dubey, and M.Blaber (2011).
A polypeptide "building block" for the β-trefoil fold identified by "top-down symmetric deconstruction".
  J Mol Biol, 407, 744-763.
PDB code: 3o3q
20516627 M.S.Chapman, and T.Somasundaram (2010).
De-icing: recovery of diffraction intensities in the presence of ice rings.
  Acta Crystallogr D Biol Crystallogr, 66, 741-744.  
19626709 H.Fu, G.R.Grimsley, A.Razvi, J.M.Scholtz, and C.N.Pace (2009).
Increasing protein stability by improving beta-turns.
  Proteins, 77, 491-498.  
19367367 T.S.Kang, and R.M.Kini (2009).
Structural determinants of protein folding.
  Cell Mol Life Sci, 66, 2341-2361.  
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