5A5W

Crystal structure of Salmonella enterica HisA D7N D176A with ProFAR

5A5W の概要

• エントリーDOI: 10.2210/pdb5a5w/pdb
• 分子名称: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase, [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[(E)-[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]amino]methylideneamino]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (3 entities in total)
• 機能のキーワード: isomerase, histidine biosynthesis, profar
• 由来する生物種: Salmonella enterica
• 細胞内の位置: Cytoplasm: A0A630AQ07
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27664.26

構造登録者

Soderholm, A.,Guo, X.,Newton, M.S.,Evans, G.B.,Nasvall, J.,Patrick, W.M.,Selmer, M. (登録日: 2015-06-23, 公開日: 2015-09-02, 最終更新日: 2024-01-10)

主引用文献

Soderholm, A.,Guo, X.,Newton, M.S.,Evans, G.B.,Nasvall, J.,Patrick, W.M.,Selmer, M.
Two-Step Ligand Binding in a Beta/Alpha8 Barrel Enzyme -Substrate-Bound Structures Shed New Light on the Catalytic Cycle of Hisa
J.Biol.Chem., 290:24657-, 2015

PubMed Abstract: HisA is a (βα)8 barrel enzyme that catalyzes the Amadori rearrangement of N'-[(5'-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (ProFAR) to N'-((5'-phosphoribulosyl) formimino)-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) in the histidine biosynthesis pathway, and it is a paradigm for the study of enzyme evolution. Still, its exact catalytic mechanism has remained unclear. Here, we present crystal structures of wild type Salmonella enterica HisA (SeHisA) in its apo-state and of mutants D7N and D7N/D176A in complex with two different conformations of the labile substrate ProFAR, which was structurally visualized for the first time. Site-directed mutagenesis and kinetics demonstrated that Asp-7 acts as the catalytic base, and Asp-176 acts as the catalytic acid. The SeHisA structures with ProFAR display two different states of the long loops on the catalytic face of the structure and demonstrate that initial binding of ProFAR to the active site is independent of loop interactions. When the long loops enclose the substrate, ProFAR adopts an extended conformation where its non-reacting half is in a product-like conformation. This change is associated with shifts in a hydrogen bond network including His-47, Asp-129, Thr-171, and Ser-202, all shown to be functionally important. The closed conformation structure is highly similar to the bifunctional HisA homologue PriA in complex with PRFAR, thus proving that structure and mechanism are conserved between HisA and PriA. This study clarifies the mechanistic cycle of HisA and provides a striking example of how an enzyme and its substrate can undergo coordinated conformational changes before catalysis.

PubMed: 26294764
DOI: 10.1074/JBC.M115.678086

実験手法

X-RAY DIFFRACTION (1.6 Å)