7TUR
Joint X-ray/neutron structure of aspastate aminotransferase (AAT) in complex with pyridoxamine 5'-phosphate (PMP)
Summary for 7TUR
| Entry DOI | 10.2210/pdb7tur/pdb |
| Descriptor | Aspartate aminotransferase, cytoplasmic, 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID, 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE, ... (4 entities in total) |
| Functional Keywords | plp-dependent enzyme, homodimer, aspartate aminotransferase, transferase |
| Biological source | Sus scrofa (pig) |
| Total number of polymer chains | 2 |
| Total formula weight | 93789.98 |
| Authors | Drago, V.N.,Kovalevsky, A.Y.,Dajnowicz, S.,Mueser, T.C. (deposition date: 2022-02-03, release date: 2022-09-28, Last modification date: 2023-10-25) |
| Primary citation | Drago, V.N.,Dajnowicz, S.,Parks, J.M.,Blakeley, M.P.,Keen, D.A.,Coquelle, N.,Weiss, K.L.,Gerlits, O.,Kovalevsky, A.,Mueser, T.C. An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction. Chem Sci, 13:10057-10065, 2022 Cited by PubMed Abstract: Pyridoxal 5'-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5'-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP N and catalytic Lys258 Nζ amino groups an equally shared deuterium is observed in an apparent low-barrier hydrogen bond (LBHB). Density functional theory calculations were performed to provide further evidence of this LBHB interaction. The structural arrangement and the juxtaposition of PMP and Lys258, facilitated by the LBHB, suggests active site preorganization for the incoming ketoacid substrate that initiates the second half-reaction. PubMed: 36128223DOI: 10.1039/d2sc02285k PDB entries with the same primary citation |
| Experimental method | NEUTRON DIFFRACTION (2.22 Å) X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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