6PU6

CobT from Methanocaldococcus jannaschii in complex with Alpha-Ribozole 5'-Phosphate, Nicotinic Acid, and Nicotinic Acid Mononucleotide

6PU6 の概要

• エントリーDOI: 10.2210/pdb6pu6/pdb
• 分子名称: UPF0284 protein MJ1598, NICOTINATE MONONUCLEOTIDE, ALPHA-RIBAZOLE-5'-PHOSPHATE, ... (5 entities in total)
• 機能のキーワード: transferase
• 由来する生物種: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 76512.50

構造登録者

Schwarzwalder, A.H.,Jeter, V.L.,Vecellio, A.A.,Erpenbach, E.,Escalante-Semerena, J.C.,Rayment, I. (登録日: 2019-07-17, 公開日: 2020-07-22, 最終更新日: 2024-04-10)

主引用文献

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

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: 36229494
DOI: 10.1038/s41598-022-21765-5

実験手法

X-RAY DIFFRACTION (2.293 Å)