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PDBsum entry 2kcf

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protein links
Isomerase PDB id
2kcf
Jmol
Contents
Protein chain
36 a.a. *
* Residue conservation analysis
PDB id:
2kcf
Name: Isomerase
Title: The nmr solution structure of the isolated apo pin1 ww domain
Structure: Peptidyl-prolyl cis-trans isomerase nima- interacting 1. Chain: a. Synonym: rotamase pin1, ppiase pin1. Engineered: yes
Source: Homo sapiens. Organism_taxid: 9606. Gene: pin1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: J.A.Kowalski,K.Liu,J.W.Kelly
Key ref: J.A.Kowalski et al. (2002). NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1. Biopolymers, 63, 111-121. PubMed id: 11786999
Date:
19-Dec-08     Release date:   13-Jan-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q13526  (PIN1_HUMAN) -  Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Seq:
Struc:
163 a.a.
36 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Biopolymers 63:111-121 (2002)
PubMed id: 11786999  
 
 
NMR solution structure of the isolated Apo Pin1 WW domain: comparison to the x-ray crystal structures of Pin1.
J.A.Kowalski, K.Liu, J.W.Kelly.
 
  ABSTRACT  
 
The NMR solution structure of the isolated Apo Pin1 WW domain (6-39) reveals that it adopts a twisted three-stranded antiparallel beta-sheet conformation, very similar to the structure exhibited by the crystal of this domain in the context of the two domain Pin1 protein. While the B factors in the apo x-ray crystal structure indicate that loop 1 and loop 2 are conformationally well defined, the solution NMR data suggest that loop 1 is quite flexible, at least in the absence of the ligand. The NMR chemical shift and nuclear Overhauser effect pattern exhibited by the 6-39 Pin1 WW domain has proven to be diagnostic for demonstrating that single site variants of this domain adopt a normally folded structure. Knowledge of this type is critical before embarking on time-consuming kinetic and thermodynamic studies required for a detailed understanding of beta-sheet folding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20036210 J.M.Rogers, L.G.Lippert, and F.Gai (2010).
Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications.
  Anal Biochem, 399, 182-189.  
19541614 A.A.Fuller, D.Du, F.Liu, J.E.Davoren, G.Bhabha, G.Kroon, D.A.Case, H.J.Dyson, E.T.Powers, P.Wipf, M.Gruebele, and J.W.Kelly (2009).
Evaluating beta-turn mimics as beta-sheet folding nucleators.
  Proc Natl Acad Sci U S A, 106, 11067-11072.
PDB code: 2kbu
19565466 M.Jäger, M.Dendle, and J.W.Kelly (2009).
Sequence determinants of thermodynamic stability in a WW domain--an all-beta-sheet protein.
  Protein Sci, 18, 1806-1813.  
18844292 M.Jager, S.Deechongkit, E.K.Koepf, H.Nguyen, J.Gao, E.T.Powers, M.Gruebele, and J.W.Kelly (2008).
Understanding the mechanism of beta-sheet folding from a chemical and biological perspective.
  Biopolymers, 90, 751-758.  
18554060 Z.Luo, J.Ding, and Y.Zhou (2008).
Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations.
  J Chem Phys, 128, 225103.  
17588228 C.S.Rapp, T.Strauss, A.Nederveen, and G.Fuentes (2007).
Prediction of protein loop geometries in solution.
  Proteins, 69, 69-74.  
17586778 M.Jäger, H.Nguyen, M.Dendle, M.Gruebele, and J.W.Kelly (2007).
Influence of hPin1 WW N-terminal domain boundaries on function, protein stability, and folding.
  Protein Sci, 16, 1495-1501.  
17766376 M.Jäger, M.Dendle, A.A.Fuller, and J.W.Kelly (2007).
A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function.
  Protein Sci, 16, 2306-2313.  
17334375 T.Peng, J.S.Zintsmaster, A.T.Namanja, and J.W.Peng (2007).
Sequence-specific dynamics modulate recognition specificity in WW domains.
  Nat Struct Mol Biol, 14, 325-331.  
17766370 T.Sharpe, A.L.Jonsson, T.J.Rutherford, V.Daggett, and A.R.Fersht (2007).
The role of the turn in beta-hairpin formation during WW domain folding.
  Protein Sci, 16, 2233-2239.  
17513360 Z.Luo, J.Ding, and Y.Zhou (2007).
Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model.
  Biophys J, 93, 2152-2161.  
16807295 M.Jäger, Y.Zhang, J.Bieschke, H.Nguyen, M.Dendle, M.E.Bowman, J.P.Noel, M.Gruebele, and J.W.Kelly (2006).
Structure-function-folding relationship in a WW domain.
  Proc Natl Acad Sci U S A, 103, 10648-10653.
PDB codes: 1zcn 2f21
17165703 Y.Fu, J.Gao, J.Bieschke, M.A.Dendle, and J.W.Kelly (2006).
Amide-to-E-olefin versus amide-to-ester backbone H-bond perturbations: Evaluating the O-O repulsion for extracting H-bond energies.
  J Am Chem Soc, 128, 15948-15949.  
15852307 C.S.Rapp, and R.M.Pollack (2005).
Crystal packing effects on protein loops.
  Proteins, 60, 103-109.  
15229605 S.Deechongkit, H.Nguyen, E.T.Powers, P.E.Dawson, M.Gruebele, and J.W.Kelly (2004).
Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics.
  Nature, 430, 101-105.  
14500877 C.M.Kraemer-Pecore, J.T.Lecomte, and J.R.Desjarlais (2003).
A de novo redesign of the WW domain.
  Protein Sci, 12, 2194-2205.  
12686540 D.M.Jacobs, K.Saxena, M.Vogtherr, P.Bernado, M.Pons, and K.M.Fiebig (2003).
Peptide binding induces large scale changes in inter-domain mobility in human Pin1.
  J Biol Chem, 278, 26174-26182.  
12651955 H.Nguyen, M.Jager, A.Moretto, M.Gruebele, and J.W.Kelly (2003).
Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation.
  Proc Natl Acad Sci U S A, 100, 3948-3953.  
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.