PDBsum entry 4j9t

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Structural genomics, unknown function PDB id
Protein chain
355 a.a.
Waters ×527
PDB id:
Name: Structural genomics, unknown function
Title: Crystal structure of a putative, de novo designed unnatural dependent metalloprotein, northeast structural genomics con target or61
Structure: Designed unnatural amino acid dependent metallopr chain: a. Synonym: neuraminidase, sialidase. Engineered: yes. Mutation: yes
Source: Micromonospora viridifaciens. Organism_taxid: 1881. Gene: neda. Expressed in: escherichia coli. Expression_system_taxid: 469008.
1.40Å     R-factor:   0.138     R-free:   0.166
Authors: F.Forouhar,S.Lew,J.Seetharaman,J.H.Mills,S.D.Khare,J.K.Evere D.Baker,G.T.Montelione,J.F.Hunt,L.Tong,Northeast Structural Consortium (Nesg)
Key ref: J.H.Mills et al. (2013). Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. J Am Chem Soc, 135, 13393-13399. PubMed id: 23924187 DOI: 10.1021/ja403503m
17-Feb-13     Release date:   27-Mar-13    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q02834  (NANH_MICVI) -  Sialidase
647 a.a.
355 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Exo-alpha-sialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     pathogenesis   1 term 
  Biochemical function     exo-alpha-sialidase activity     1 term  


DOI no: 10.1021/ja403503m J Am Chem Soc 135:13393-13399 (2013)
PubMed id: 23924187  
Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.
J.H.Mills, S.D.Khare, J.M.Bolduc, F.Forouhar, V.K.Mulligan, S.Lew, J.Seetharaman, L.Tong, B.L.Stoddard, D.Baker.
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 importance 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 Co(2+), Zn(2+), Fe(2+), and Ni(2+), with a Kd for Zn(2+) of ∼40 pM. X-ray crystal structures of the designed protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 Å respectively over all atoms in the binding site.