NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima

Abstract

and the backboneatom root-mean-square deviation (RMSD) value of 0.35 Afor the best 20 DYANA conformers after energy-minimiza-tion [Fig. 1(A) and Table I] are representative of a high-quality structure determination. The structure of TM1816contains 3 -helices and a 5-stranded -sheet. The se-quence arrangement of the regular secondary structures, [Fig. 1(A and B)], is similar to that of theribonuclease H superfamily. The -sheet is comprised ofthe residues Met 1–Val 7 ( 1), Tyr 26–Val 32 ( 2), Val39–Glu44( 3),Leu67–Val70( 4),andLys87–Ile89( 5)with topology 54123. Strand 1 is parallel to 3, 4, and 5, and antiparallel to 2. The helices 1 (residues 56–62)and 2 (residues 75–84) are arranged in parallel on oneface of the -sheet, and 3 (residues 96–105) is approxi-mately perpendicular to 1 and 2 on the opposite face ofthe -sheet. The loop connecting 1 and 2 (L1; Figs. 1(B)and 2(A)] is 19 residues long, with several hydrogen bondsand hydrophobic residue contacts that tether it to the restof the structure.The crystal structure of TM1816, which includes a12-amino acid N-terminal tag [Protein Data Bank (PDB)ID: 1O13], was also determined by the JCSG. The NMRand X-ray structures are very similar, with the residues4–43 and 55–110 superimposable with a pairwise back-bone RMSD of 1.1 A [Fig. 1(C)]. The regions with thelargest variations are loop L3 and helix 3. Loop L3 [Figs.1(B) and 2(A)], which is disordered in the NMR structure[Fig. 1(A)], is well-ordered in the crystal structure. Anumber of crystal contacts seem to account for thesevariationsbetweentheNMRandX-raystructures.Specifi-cally, intermolecular interactions of loop L1 and strand 3are found with loop L3 of a symmetry-related molecule,which includes formation of a short intermolecular paral-lel -sheet between strand 3 (residues 38–42) and loopL3 (residues 51–54). Additional intermolecular contactsare made between loop L2 and helix 3.TM1816 belongs to the Cluster of Orthologous Group(COG) 1433, which contains 28 functionally uncharacter-izedconservedproteinsfrom13differentorganisms,whichare predominantly archaeal species. The structures of 2other COG 1433 members, MTH1175