7VRX

Pad-1 in the absence of substrate

Summary for 7VRX

• Entry DOI: 10.2210/pdb7vrx/pdb
• Descriptor: Aminotransferase, SULFATE ION (3 entities in total)
• Functional Keywords: auxin homeostasis, indole-3-pyruvic acid aminotransferase, substrate specificity, transferase
• Biological source: Solanum melongena (Eggplant, Aubergine)
• Total number of polymer chains: 4
• Total formula weight: 180539.25

Authors

Choi, M.,Rhee, S. (deposition date: 2021-10-25, release date: 2022-04-20, Last modification date: 2023-11-29)

Primary citation

Choi, M.,Rhee, S.
Structural and biochemical basis for the substrate specificity of Pad-1, an indole-3-pyruvic acid aminotransferase in auxin homeostasis.
J.Struct.Biol., 214:107857-107857, 2022

PubMed Abstract: Phytohormone indole-3-acetic acid (IAA) plays a vital role in regulating plant growth and development. Tryptophan-dependent IAA biosynthesis participates in IAA homeostasis by producing IAA via two sequential reactions, which involve a conversion of tryptophan to indole-3-pyruvic acid (IPyA) by tryptophan aminotransferase (TAA1) followed by the irreversible formation of IAA in the second reaction. Pad-1 from Solanaceae plants regulates IAA levels by catalyzing a reverse reaction of the first step of IAA biosynthesis. Pad-1 is a pyridoxal phosphate (PLP)-dependent aminotransferase, with IPyA as the amino acceptor and l-glutamine as the amino donor. Currently, the structural and functional basis for the substrate specificity of Pad-1 remains poorly understood. In this study, we carried out structural and kinetic analyses of Pad-1 from Solanum melongena. Pad-1 is a homodimeric enzyme, with coenzyme PLP present between a central large α/β domain and a protruding small domain. The active site of Pad-1 includes a vacancy near the phosphate group (P-side) and the 3'-O (O-side) of PLP. These features are distinct from those of TAA1, which is homologous in an overall structure with Pad-1 but includes only the P-side region in the active site. Kinetic analysis suggests that P-side residues constitute a binding pocket for l-glutamine, and O-side residues of Phe124 and Ile350 are involved in the binding of IPyA. These studies illuminate distinct differences in the active site between Pad-1 and TAA1, and provide structural and functional insights into the substrate specificity of Pad-1.

PubMed: 35395410
DOI: 10.1016/j.jsb.2022.107857

Experimental method

X-RAY DIFFRACTION (1.96634676226 Å)