1K5R

YAP65 WW domain S24-Amino-Ethylsulfanyl-Acetic Acid mutant


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.

Ferguson, N.Pires, J.R.Toepert, F.Johnson, C.M.Pan, Y.P.Volkmer-Engert, R.Schneider-Mergener, J.Daggett, V.Oschkinat, H.Fersht, A.

(2001) Proc Natl Acad Sci U S A 98: 13008-13013

  • DOI: 10.1073/pnas.221467398
  • Primary Citation of Related Structures:  
    1K5R

  • PubMed Abstract: 
  • Chemical synthesis allows the incorporation of nonnatural amino acids into proteins that may provide previously untried probes of their folding pathway and thermodynamic stability. We have used a flexible thioether linker as a loop mimetic in the hum ...

    Chemical synthesis allows the incorporation of nonnatural amino acids into proteins that may provide previously untried probes of their folding pathway and thermodynamic stability. We have used a flexible thioether linker as a loop mimetic in the human yes kinase-associated protein (YAP 65) WW domain, a three-stranded, 44-residue, beta-sheet protein. This linkage avoids problems of incorporating sequences that constrain loops to the extent that they significantly change the nature of the denatured state with concomitant effects on the folding kinetics. An NMR solution structure shows that the thioether linker had little effect on the global fold of the domain, although the loop is apparently more dynamic. The thioether variants are destabilized by up to 1.4 kcal/mol (1 cal = 4.18 J). Preliminary Phi-value analysis showed that the first loop is highly structured in the folding transition state, and the second loop is essentially unstructured. These data are consistent with results from simulated unfolding and detailed protein-engineering studies of structurally homologous WW domains. Previously, Phi-value analysis was limited to studying side-chain interactions. The linkers used here extend the protein engineering method directly to secondary-structure interactions.


    Organizational Affiliation

    Medical Research Council, Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
65 KDA YES-ASSOCIATED PROTEINA41N/AMutation(s): 1 
Find proteins for P46937 (Homo sapiens)
Explore P46937 
Go to UniProtKB:  P46937
NIH Common Fund Data Resources
PHAROS  P46937
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fragment of WBP-1B10N/AMutation(s): 0 
Find proteins for Q96G27 (Homo sapiens)
Explore Q96G27 
Go to UniProtKB:  Q96G27
NIH Common Fund Data Resources
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 1K5R Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance