7E4G

Crystal structure of schizorhodopsin 4

Summary for 7E4G

• Entry DOI: 10.2210/pdb7e4g/pdb
• Descriptor: schizorhodopsin 4, ZINC ION, SULFATE ION, ... (6 entities in total)
• Functional Keywords: rhodopsin, inward proton pump, membrane protein
• Biological source: Asgard group archaeon
• Total number of polymer chains: 3
• Total formula weight: 86365.53

Authors

Shihoya, W.,Nureki, O. (deposition date: 2021-02-12, release date: 2021-02-24, Last modification date: 2024-11-06)

Primary citation

Higuchi, A.,Shihoya, W.,Konno, M.,Ikuta, T.,Kandori, H.,Inoue, K.,Nureki, O.
Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: Schizorhodopsins (SzRs), a new rhodopsin family identified in Asgard archaea, are phylogenetically located at an intermediate position between type-1 microbial rhodopsins and heliorhodopsins. SzRs work as light-driven inward H pumps as xenorhodopsins in bacteria. Although E81 plays an essential role in inward H release, the H is not metastably trapped in such a putative H acceptor, unlike the other H pumps. It remains elusive why SzR exhibits different kinetic behaviors in H release. Here, we report the crystal structure of SzR AM_5_00977 at 2.1 Å resolution. The SzR structure superimposes well on that of bacteriorhodopsin rather than heliorhodopsin, suggesting that SzRs are classified with type-1 rhodopsins. The structure-based mutagenesis study demonstrated that the residues N100 and V103 around the β-ionone ring are essential for color tuning in SzRs. The cytoplasmic parts of transmembrane helices 2, 6, and 7 are shorter than those in the other microbial rhodopsins, and thus E81 is located near the cytosol and easily exposed to the solvent by light-induced structural change. We propose a model of untrapped inward H release; H is released through the water-mediated transport network from the retinal Schiff base to the cytosol by the side of E81. Moreover, most residues on the H transport pathway are not conserved between SzRs and xenorhodopsins, suggesting that they have entirely different inward H release mechanisms.

PubMed: 33790007
DOI: 10.1073/pnas.2016328118

Experimental method

X-RAY DIFFRACTION (2.1 Å)