The solution structure of ribosomal protein L36 from Thermus thermophilus reveals a zinc-ribbon-like fold

We have determined the solution NMR structure of the ribosomal protein L36 from Thermus thermophilus. L36 is the smallest protein in the large subunit of the prokaryotic ribosome. The sequence contains three completely conser ved cysteine residues and one conserved histidine residue in a C-X-2-C-X-12 -C-X-4-H motif. Extended X-ray absorption fine structure spectroscopy was u sed to confirm that a purified L36 sample contains an equimolar amount of z inc. The structure of L36 was determined using simulated annealing based on NOE distance restraints, dihedral angle restraints and hydrogen bond dista nce restraints derived from NMR spectra of N-15-labeled and non-labeled L36 samples at pH 7 and 12 degrees C, and by imposing tetrahedral zinc ion coo rdination geometry. The L36 fold is characterized by a triple-stranded anti parallel P-sheet with the zinc-binding site at one end. The structure of th e zinc site is well-determined and shows that the three cysteine sulphur at oms are supported by hydrogen bonds to backbone amide protons. The conserve d histidine residue is located in a short 3(10)-helix and coordinates zinc by the N-delta 1 atom. The electrostatic surface potential and location of conserved Arg, Lys and His side-chains suggest a large continuous L36-rRNA interaction interface. The folding topology as well as position and conform ation of many conserved side-chains in L36 are very similar to those of zin c-ribbon domains found in the archaeal transcription factor TFIIB N terminu s and the eukaryal transcription elongation factor hTFIIS C terminus. Given the relative antiquity of the ribosome it is possible that L36 reflects th e parent of transcription-related zinc ribbons. (C) 2000 Academic Press.