1NVO

Solution structure of a four-helix bundle model, apo-DF1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Preorganization of molecular binding sites in designed diiron proteins

Maglio, O.Nastri, F.Pavone, V.Lombardi, A.DeGrado, W.F.

(2003) Proc.Natl.Acad.Sci.USA 100: 3772-3777

  • DOI: 10.1073/pnas.0730771100
  • Also Cited By: 2KIK, 1U7M, 1U7J

  • PubMed Abstract: 
  • De novo protein design provides an attractive approach to critically test the features that are required for metalloprotein structure and function. Previously we designed and crystallographically characterized an idealized dimeric model for the four- ...

    De novo protein design provides an attractive approach to critically test the features that are required for metalloprotein structure and function. Previously we designed and crystallographically characterized an idealized dimeric model for the four-helix bundle class of diiron and dimanganese proteins [Dueferri 1 (DF1)]. Although the protein bound metal ions in the expected manner, access to its active site was blocked by large bulky hydrophobic residues. Subsequently, a substrate-access channel was introduced proximal to the metal-binding center, resulting in a protein with properties more closely resembling those of natural enzymes. Here we delineate the energetic and structural consequences associated with the introduction of these binding sites. To determine the extent to which the binding site was preorganized in the absence of metal ions, the apo structure of DF1 in solution was solved by NMR and compared with the crystal structure of the di-Zn(II) derivative. The overall fold of the apo protein was highly similar to that of the di-Zn(II) derivative, although there was a rotation of one of the helices. We also examined the thermodynamic consequences associated with building a small molecule-binding site within the protein. The protein exists in an equilibrium between folded dimers and unfolded monomers. DF1 is a highly stable protein (K(diss) = 0.001 fM), but the dissociation constant increases to 0.6 nM (deltadeltaG = 5.4 kcalmol monomer) as the active-site cavity is increased to accommodate small molecules.


    Related Citations: 
    • Toward the De Novo Design of a Catalytically Active Helix Bundle: a Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center
      Di Costanzo, L.,Wade, H.,Geremia, S.,Randaccio, L.,Pavone, V.,DeGrado, W.F.,Lombardi, A.
      (2001) J.Am.Chem.Soc. 123: 12749
    • Tertiary Templates for the Design of Diiron Protein
      Summa, C.M.,Lombardi, A.,Lewis, M.,DeGrado, W.F.
      (1999) CURR.OPIN.STRUCT.BIOL. 9: 500
    • Retrostructural Analysis of Metalloproteins. Application to the Design of a Minimal Model for Diiron Proteins
      Lombardi, A.,Summa, C.M.,Geremia, S.,Randaccio, L.,Pavone, V.,DeGrado, W.F.
      (2000) Proc.Natl.Acad.Sci.USA 97: 6298
    • Sliding Helix and Change of Coordination Geometry in a Model di-Mn(II) Protein
      DeGrado, W.F.,Di Costanzo, L.,Geremia, S.,Lombardi, A.,Pavone, V.,Randaccio, L.
      (2003) Angew.Chem.Int.Ed.Engl. 42: 417


    Organizational Affiliation

    Department of Chemistry, University of Napoli Federico II, Complesso Universitario Monte S. Angelo, I-80126 Napoli, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homodimeric Alpha2 Four-Helix Bundle
A, B
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B
NON-POLYMERH2 N

--

ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy 
  • Olderado: 1NVO Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance