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PDBsum entry 1idz

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protein links
DNA-binding protein PDB id
1idz
Jmol
Contents
Protein chain
54 a.a. *
* Residue conservation analysis
PDB id:
1idz
Name: DNA-binding protein
Title: Structure of myb transforming protein, nmr, 20 structures
Structure: MousE C-myb DNA-binding domain repeat 3. Chain: a. Engineered: yes. Mutation: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: K.Furukawa,M.Oda,H.Nakamura
Key ref: K.Furukawa et al. (1996). A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy. Proc Natl Acad Sci U S A, 93, 13583-13588. PubMed id: 8942977
Date:
15-Aug-96     Release date:   23-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06876  (MYB_MOUSE) -  Transcriptional activator Myb
Seq:
Struc:
 
Seq:
Struc:
636 a.a.
54 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     chromatin binding     2 terms  

 

 
Proc Natl Acad Sci U S A 93:13583-13588 (1996)
PubMed id: 8942977  
 
 
A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy.
K.Furukawa, M.Oda, H.Nakamura.
 
  ABSTRACT  
 
A small globular protein, the third repeat of the c-Myb DNA-binding domain, which is composed of 54 amino acid residues, was engineered so as to understand the structural uniqueness of native proteins. This small protein has three alpha-helices that form a helix-turn-helix structure, which is maintained by the hydrophobic core with three Ile residues. One of the mutant proteins, with two of the buried Ile (Ile-155 and Ile-181) substituted with Leu residues, showed multiple conformations, as monitored by heteronuclear magnetic resonance spectroscopy for 13C- and 15N-labeled proteins. The increase in the side-chain conformational entropy, caused by changing the Ile to a Leu residue on an alpha-helix, could engender the lack of structural uniqueness. In native proteins, the conformations of not only the beta-branched side chains, but also those of the neighboring bulky side chains, can be greatly restricted, depending upon the local backbone structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19445951 B.G.Wensley, M.Gärtner, W.X.Choo, S.Batey, and J.Clarke (2009).
Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms.
  J Mol Biol, 390, 1074-1085.  
17855563 J.López de la Osa, D.A.Bateman, S.Ho, C.González, A.Chakrabartty, and D.V.Laurents (2007).
Getting specificity from simplicity in putative proteins from the prebiotic earth.
  Proc Natl Acad Sci U S A, 104, 14941-14946.
PDB codes: 2jo4 2jo5
14595026 S.Gianni, N.R.Guydosh, F.Khan, T.D.Caldas, U.Mayor, G.W.White, M.L.DeMarco, V.Daggett, and A.R.Fersht (2003).
Unifying features in protein-folding mechanisms.
  Proc Natl Acad Sci U S A, 100, 13286-13291.  
11093263 S.Takada (2001).
Protein folding simulation with solvent-induced force field: folding pathway ensemble of three-helix-bundle proteins.
  Proteins, 42, 85-98.  
  10752620 O.V.Galzitskaya, A.K.Surin, and H.Nakamura (2000).
Optimal region of average side-chain entropy for fast protein folding.
  Protein Sci, 9, 580-586.  
10801318 Y.Isogai, A.Ishii, T.Fujisawa, M.Ota, and K.Nishikawa (2000).
Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties.
  Biochemistry, 39, 5683-5690.  
10360940 Y.Isogai, M.Ota, T.Fujisawa, H.Izuno, M.Mukai, H.Nakamura, T.Iizuka, and K.Nishikawa (1999).
Design and synthesis of a globin fold.
  Biochemistry, 38, 7431-7443.  
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.