6DRF

Structure of human Retinal Degeneration 3(RD3) Protein

Summary for 6DRF

• Entry DOI: 10.2210/pdb6drf/pdb
• NMR Information: BMRB: 27305
• Descriptor: Protein RD3 (1 entity in total)
• Functional Keywords: sensory transduction, vision, signaling protein
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 16601.79

Authors

Yu, Q.,Lim, S.,Peshenko, I.,Cudia, D.,Dizhoor, A.M.,Ames, J.B. (deposition date: 2018-06-11, release date: 2019-02-06, Last modification date: 2024-05-15)

Primary citation

Peshenko, I.V.,Yu, Q.,Lim, S.,Cudia, D.,Dizhoor, A.M.,Ames, J.B.
Retinal degeneration 3 (RD3) protein, a retinal guanylyl cyclase regulator, forms a monomeric and elongated four-helix bundle.
J. Biol. Chem., 294:2318-2328, 2019

PubMed Abstract: Retinal degeneration 3 (RD3) protein promotes accumulation of retinal membrane guanylyl cyclase (RetGC) in the photoreceptor outer segment and suppresses RetGC activation by guanylyl cyclase-activating proteins (GCAPs). Mutations truncating RD3 cause severe congenital blindness by preventing the inhibitory binding of RD3 to the cyclase. The high propensity of RD3 to aggregate in solution has prevented structural analysis. Here, we produced a highly soluble variant of human RD3 (residues 18-160) that is monomeric and can still bind and negatively regulate RetGC. The NMR solution structure of RD3 revealed an elongated backbone structure (70 Å long and 30 Å wide) consisting of a four-helix bundle with a long unstructured loop between helices 1 and 2. The structure reveals that RD3 residues previously implicated in the RetGC binding map to a localized and contiguous area on the structure, involving a loop between helices 2 and 3 and adjacent parts of helices 3 and 4. The NMR structure of RD3 was validated by mutagenesis. Introducing Trp or Phe to replace Cys or Leu, respectively, disrupts packing in the hydrophobic core and lowers RD3's apparent affinity for RetGC1. Introducing a positive charge at the interface (Glu to Lys) also lowered the affinity. Conversely, introducing Val in place of Cys stabilized the hydrophobic core and increased the RD3 affinity for the cyclase. The NMR structure of RD3 presented here provides a structural basis for elucidating RD3-RetGC interactions relevant for normal vision or blindness.

PubMed: 30559291
DOI: 10.1074/jbc.RA118.006106

Experimental method

SOLUTION NMR