1nvo

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|PDB= 1nvo |SIZE=350|CAPTION= <scene name='initialview01'>1nvo</scene>
|PDB= 1nvo |SIZE=350|CAPTION= <scene name='initialview01'>1nvo</scene>
|SITE=
|SITE=
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|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene> and <scene name='pdbligand=NH2:AMINO GROUP'>NH2</scene>
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|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>
|ACTIVITY=
|ACTIVITY=
|GENE=
|GENE=
 +
|DOMAIN=
 +
|RELATEDENTRY=[[1ec5|1EC5]], [[1jmb|1JMB]], [[1jm0|1JM0]], [[1lt1|1LT1]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nvo OCA], [http://www.ebi.ac.uk/pdbsum/1nvo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nvo RCSB]</span>
}}
}}
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[[Category: Nastri, F.]]
[[Category: Nastri, F.]]
[[Category: Pavone, V.]]
[[Category: Pavone, V.]]
-
[[Category: ACE]]
 
-
[[Category: NH2]]
 
[[Category: alpha-helical bundle]]
[[Category: alpha-helical bundle]]
[[Category: de novo protein design]]
[[Category: de novo protein design]]
[[Category: diiron protein model]]
[[Category: diiron protein model]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:02:21 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:36:11 2008''

Revision as of 19:36, 30 March 2008


PDB ID 1nvo

Drag the structure with the mouse to rotate
Ligands: ,
Related: 1EC5, 1JMB, 1JM0, 1LT1


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



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


Overview

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.

About this Structure

1NVO is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Preorganization of molecular binding sites in designed diiron proteins., Maglio O, Nastri F, Pavone V, Lombardi A, DeGrado WF, Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3772-7. Epub 2003 Mar 24. PMID:12655072

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