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PDBsum entry 1k5u

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Hormone/growth factor PDB id
1k5u
Jmol PyMol
Contents
Protein chains
129 a.a. *
Ligands
SO4 ×3
Waters ×83
* Residue conservation analysis
PDB id:
1k5u
Name: Hormone/growth factor
Title: Human acidic fibroblast growth factor. 141 amino acid form with amino terminal his tag with his93 replaced by gly (h93g).
Structure: Acidic fibroblast growth factor. Chain: a, b, c. Engineered: yes. Mutation: yes. Other_details: amino terminal his tag
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.00Å     R-factor:   0.233     R-free:   0.293
Authors: J.Kim,S.I.Blaber,M.Blaber
Key ref:
J.Kim et al. (2002). Alternative type I and I' turn conformations in the beta8/beta9 beta-hairpin of human acidic fibroblast growth factor. Protein Sci, 11, 459-466. PubMed id: 11847269 DOI: 10.1110/ps.43802
Date:
12-Oct-01     Release date:   27-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   9 terms 
  Biological process     phosphatidylinositol-3-phosphate biosynthetic process   36 terms 
  Biochemical function     S100 protein binding     11 terms  

 

 
DOI no: 10.1110/ps.43802 Protein Sci 11:459-466 (2002)
PubMed id: 11847269  
 
 
Alternative type I and I' turn conformations in the beta8/beta9 beta-hairpin of human acidic fibroblast growth factor.
J.Kim, S.I.Blaber, M.Blaber.
 
  ABSTRACT  
 
Human acidic fibroblast growth factor (FGF-1) has a beta-trefoil structure, one of the fundamental protein superfolds. The X-ray crystal structures of wild-type and various mutant forms of FGF-1 have been solved in five different space groups: C2, C222(1), P2(1) (four molecules/asu), P2(1) (three molecules/asu), and P2(1)2(1)2(1). These structures reveal two characteristically different conformations for the beta8/beta9 beta-hairpin comprising residue positions 90-94. This region in the wild-type FGF-1 structure (P2(1), four molecules/asu), a his-tagged His93-->Gly mutant (P2(1), three molecules/asu) and a his-tagged Asn106-->Gly mutant (P2(1)2(1)2(1)) adopts a 3:5 beta-hairpin known as a type I (1-4) G1 beta-bulge (containing a type I turn). However, a his-tagged form of wild-type FGF-1 (C222(1)) and a his-tagged Leu44-->Phe mutant (C2) adopt a 3:3 beta-hairpin (containing a type I' turn) for this same region. A feature that distinguishes these two types of beta-hairpin structures is the number and location of side chain positions with eclipsed C(beta) and main-chain carbonyl oxygen groups (Psi is equivalent to +60 degrees). The effects of glycine mutations upon stability, at positions within the hairpin, have been used to identify the most likely structure in solution. Type I' turns in the structural data bank are quite rare, and a survey of these turns reveals that a large percentage exhibit crystal contacts within 3.0 A. This suggests that many of the type I' turns in X-ray structures may be adopted due to crystal packing effects.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Relaxed stereodiagram of human FGF-1 (Blaber et al. 1996) showing the location of the 8/9 turn region and the 90-94 -hairpin (dark gray). The view is down the pseudo threefold axis of symmetry present in the -trefoil architecture. Region 90-94 is related to the N- and C-termini by this internal symmetry.
Figure 4.
Fig. 4. Distribution of the distances between type I` turns and crystal contacts from 116 type I` turns in the structural databank.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2002, 11, 459-466) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15632285 J.Kim, J.Lee, S.R.Brych, T.M.Logan, and M.Blaber (2005).
Sequence swapping does not result in conformation swapping for the beta4/beta5 and beta8/beta9 beta-hairpin turns in human acidic fibroblast growth factor.
  Protein Sci, 14, 351-359.
PDB codes: 1pzz 1q03 1q04
14627732 S.R.Brych, J.Kim, T.M.Logan, and M.Blaber (2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
  Protein Sci, 12, 2704-2718.
PDB codes: 1jy0 1m16 1nzk 1p63
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 codes are shown on the right.

 

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