Macromolecule Content

• Total Structure Weight: 5695.36 
• Atom Count: 402 
• Residue Count: 51 
• Unique protein chains: 2

1K5R

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

• DOI: 10.2210/pdb1K5R/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens


• Deposited: 2001-10-12 Released: 2001-11-02 
• Deposition Author(s): 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.R.

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Experimental Data Snapshot

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

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.USA 98: 13008-13013

• PubMed: 11687614 
• DOI: 10.1073/pnas.221467398


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
65 KDA YES-ASSOCIATED PROTEIN	A	41	Homo sapiens	Mutation(s): 0  Gene Names: YAP1 (YAP65)
Find proteins for P46937 (Homo sapiens) Go to Gene View: YAP1 Go to UniProtKB:  P46937

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fragment of WBP-1	B	10	Homo sapiens	Mutation(s): 0  Gene Names: WBP1
Find proteins for Q96G27 (Homo sapiens) Go to Gene View: WBP1 Go to UniProtKB:  Q96G27

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NH2	A	NON-POLYMER	H2 N		--
ESD	A	NON-POLYMER	C4 H9 N O2 S		--

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

Entry History 

Deposition Data

• Deposited Date: 2001-10-12 
• Released Date: 2001-11-02 
• Deposition Author(s): 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.R.

Revision History 

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