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4j9t

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4j9t, resolution 1.40Å ()
Ligands: ,
Gene: nedA (Micromonospora viridifaciens)
Related: 1eus


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


Contents

Crystal structure of a putative, de novo designed unnatural amino acid dependent metalloprotein, northeast structural genomics consortium target OR61

Publication Abstract from PubMed

Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation, and the identities and orientations of surrounding residues represents a formidable challenge. Computational design methods have been used to identify optimal locations for functional sites in proteins and design the surrounding residues, but have not incorporated unnatural amino acids in this process. We extended the Rosetta design methodology to design metalloproteins in which the amino acid (2,2'-bipyridin-5yl)alanine (Bpy-Ala) is a primary ligand of a bound metal ion. Following initial results that indicated the im-portance of buttressing the Bpy-Ala amino acid, we designed a buried metal binding site with octahedral coordination geometry consisting of Bpy-Ala, two protein based metal ligands, and two metal bound water molecules. Experimental characterization revealed a Bpy-Ala mediated metalloprotein with the ability to bind divalent cations including Co2+, Zn2+, Fe2+, and Ni2+, with a Kd for Zn2+ of ~40 pM. X-ray crystallograph-ic analysis of the designed protein shows only slight deviation from the computationally designed model.

Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy., Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D, J Am Chem Soc. 2013 Aug 7. PMID:23924187

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Function

[NANH_MICVI] To release sialic acids for use as carbon and energy sources for this non-pathogenic bacterium while in pathogenic microorganisms, sialidases have been suggested to be pathogenic factors.

About this Structure

4j9t is a 1 chain structure with sequence from Micromonospora viridifaciens. Full crystallographic information is available from OCA.

Reference

  • Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy. J Am Chem Soc. 2013 Aug 7. PMID:23924187 doi:10.1021/ja403503m

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