Reprogramming receptors to artificially respond to light has strong potential for molecular studies and interrogation of biological functions. Here, we design a light-controlled ionotropic glutamate receptor by genetically encoding a photoreactive unnatural amino acid (UAA). The photo-cross-linker p-azido-L-phenylalanine (AzF) was encoded in NMDA receptors (NMDARs), a class of glutamate-gated ion channels that play key roles in neuronal development and plasticity. AzF incorporation in the obligatory GluN1 subunit at the GluN1/GluN2B N-terminal domain (NTD) upper lobe dimer interface leads to an irreversible allosteric inhibition of channel activity upon UV illumination. In contrast, when pairing the UAA-containing GluN1 subunit with the GluN2A subunit, light-dependent inactivation is completely absent. By combining electrophysiological and biochemical analyses, we identify subunit-specific structural determinants at the GluN1/GluN2 NTD dimer interfaces that critically dictate UV-controlled inactivation. Our work reveals that the two major NMDAR subtypes differ in their ectodomain-subunit interactions, in particular their electrostatic contacts, resulting in GluN1 NTD coupling more tightly to the GluN2B NTD than to the GluN2A NTD. It also paves the way for engineering light-sensitive ligand-gated ion channels with subtype specificity through the genetic code expansion.neurotransmitter receptor | protein structure-function I ntroducing light-sensitive moieties into proteins provides a powerful approach to investigate molecular mechanisms as well as biological functions with high temporal and spatial resolution (1, 2). An attractive strategy to engineer light responsiveness relies on the use of photoreactive unnatural amino acids (UAAs), allowing site-specific incorporation in a protein target. The methodology relies on the read-through of an unassigned codon (commonly the amber stop codon) in an mRNA by a suppressor tRNA aminoacylated with a desired UAA. Using this approach, UAAs with unique chemical functionalities including light-sensitivity have been successfully incorporated into ion channels and neurotransmitter receptors, significantly contributing to our understanding of receptor function (3, 4). However, the challenging synthesis of the chemically acylated tRNA has limited the general applicability of the approach. The recent development of genetically engineered suppressor tRNA/ aminoacyl-tRNA synthetase pairs with altered amino acid specificity allowed for aminoacylation in the expression system in situ. This method provided a major step forward by advancing the UAA technology to the all-genetic-based level, also known as "the genetic-code expansion" (5-7).Here, we present the design of a light-sensitive ionotropic glutamate receptor (iGluR) through the genetic incorporation of a photoreactive UAA. Our approach takes advantage of the recent development of the genetic-code expansion in Xenopus oocytes (8), which is a classical vehicle for heterologous expression and functional characterization of ligand-g...