5EDD
Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant
Summary for 5EDD
| Entry DOI | 10.2210/pdb5edd/pdb |
| Related | 2PY4 3H6D 3HZA 3I93 3LOJ 4GCY |
| Descriptor | Deoxyuridine 5'-triphosphate nucleotidohydrolase, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, ... (5 entities in total) |
| Functional Keywords | jelly-roll, enzyme-ligand complex, hydrolase |
| Biological source | Mycobacterium tuberculosis |
| Total number of polymer chains | 1 |
| Total formula weight | 18625.97 |
| Authors | Nagy, G.N.,Leveles, I.,Lopata, A.,Harmat, V.,Toth, J.,Vertessy, G.B. (deposition date: 2015-10-21, release date: 2016-11-02, Last modification date: 2024-01-10) |
| Primary citation | Nagy, G.N.,Suardiaz, R.,Lopata, A.,Ozohanics, O.,Vekey, K.,Brooks, B.R.,Leveles, I.,Toth, J.,Vertessy, B.G.,Rosta, E. Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. J. Am. Chem. Soc., 138:15035-15045, 2016 Cited by PubMed Abstract: Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the γ-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all of the above properties; all essential arginine fingers are used to catalyze the cleavage of the γ-phosphate. Here, we identify and unveil the role of a conserved arginine residue in trimeric dUTPases that meets all the criteria established for arginine fingers. We found that the conserved arginine adjacent to the P-loop-like motif enables structural organization of the active site for efficient catalysis via its nucleotide coordination, while its direct electrostatic role in transition state stabilization is secondary. An exhaustive structure-based comparison of analogous, conserved arginines from nucleotide hydrolases and transferases revealed a consensus amino acid location and orientation for contacting the γ-phosphate of the substrate nucleotide. Despite the structurally equivalent position, functional differences between arginine fingers of dUTPases and NTPases are explained on the basis of the unique chemistry performed by the pyrophosphatase dUTPases. PubMed: 27740761DOI: 10.1021/jacs.6b09012 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.97 Å) |
Structure validation
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