6PU6
CobT from Methanocaldococcus jannaschii in complex with Alpha-Ribozole 5'-Phosphate, Nicotinic Acid, and Nicotinic Acid Mononucleotide
Summary for 6PU6
| Entry DOI | 10.2210/pdb6pu6/pdb |
| Descriptor | UPF0284 protein MJ1598, NICOTINATE MONONUCLEOTIDE, ALPHA-RIBAZOLE-5'-PHOSPHATE, ... (5 entities in total) |
| Functional Keywords | transferase |
| Biological source | Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) |
| Total number of polymer chains | 2 |
| Total formula weight | 76512.50 |
| Authors | Schwarzwalder, A.H.,Jeter, V.L.,Vecellio, A.A.,Erpenbach, E.,Escalante-Semerena, J.C.,Rayment, I. (deposition date: 2019-07-17, release date: 2020-07-22, Last modification date: 2024-04-10) |
| Primary citation | Jeter, V.L.,Schwarzwalder, A.H.,Rayment, I.,Escalante-Semerena, J.C. Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria. Sci Rep, 12:17175-17175, 2022 Cited by PubMed Abstract: Cobamides (Cbas) are coenzymes used by cells across all domains of life, but de novo synthesis is only found in some bacteria and archaea. Five enzymes assemble the nucleotide loop in the alpha phase of the corrin ring. Condensation of the activated ring and nucleobase yields adenosyl-Cba 5'-phosphate, which upon dephosphorylation yields the biologically active coenzyme (AdoCba). Base activation is catalyzed by a phosphoribosyltransferase (PRTase). The structure of the Salmonella enterica PRTase enzyme (i.e., SeCobT) is well-characterized, but archaeal PRTases are not. To gain insights into the mechanism of base activation by the PRTase from Methanocaldococcus jannaschii (MjCobT), we solved crystal structures of the enzyme in complex with substrate and products. We determined several structures: (i) a 2.2 Å structure of MjCobT in the absence of ligand (apo), (ii) structures of MjCobT bound to nicotinate mononucleotide (NaMN) and α-ribazole 5'-phosphate (α-RP) or α-adenylyl-5'-phosphate (α-AMP) at 2.3 and 1.4 Å, respectively. In MjCobT the general base that triggers the reaction is an aspartate residue (Asp 52) rather than a glutamate residue (E317) as in SeCobT. Notably, the dimer interface in MjCobT is completely different from that observed in SeCobT. Finally, entry PDB 3L0Z does not reflect the correct structure of MjCobT. PubMed: 36229494DOI: 10.1038/s41598-022-21765-5 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.293 Å) |
Structure validation
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