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The structure was based on the mitochondrial aldehyde dehydrogenase type two. RalDH2 in a monomer made up of 3 domains: a nucleotide-binding domain (1-136, 161-270), a catalytic domain (271-484), and a tetramerization domain (137-160, 485-484) as shown in Figure 1.^[1]

The tetramer can be envisioned as an "X", with nucleotide-binding sites at the tips of the "X", and the tetramerization domains as the equatorial portion of the "X" as seen in Figure 2.^[1] The is presented by the alpha1 helix and beta11 strand of one nucleotide-binding domain, with the same alpha1 helix and beta11 strand of it's dimer (Figure 2, the purple highlighted region). Although the beta strands are far apart, ordered water molecules are present to create beta-sheet contacts.^[1] The is presented by the beta18 of the catalytic domain beta-sheet of one monomer and the beta19 of the tetramerization domain of it's dimer(Figure 2, the pink highlighted region).^[1] This dimerization interaction creates an "embrace" between the beta-sheet's contact, and creates a channel for the substrate to access the active site.^[1]

Cofactor NAD and Cl ions

The crystal structure was cocrystallized with , and was determined at a 2.7 Angstrom resolution (Figure 2 Chain D present with NAD represented in pink).^[1] NAD+ acts as a cofactor and is the electron acceptor in RalDH2 oxidoructase reaction as seen in the reaction presented above. RalDH2 has to be folded in a proper manner for its enzymatic function to occur. The folding of the enzyme is partially due to the interactions of NAD+ and Chloride ions. When NAD+ is present hydrogen bonds with Glu and Ser form, van der Waals interactions with non-polar residues and one polar residue (Lys) forms. The interaction with Lys-192 provides the transition state stability, making for a favorable confirmation.^[1] This conformational change is important since in the absence of NAD+, no crystal structures grew in any of the screened conditions.^[1] The Chloride ions participate in hydrophobic interactions with Arg which also help maintain the folded structure.^[1] With the cofactor NAD+ present the catalytic domain of RalDH2 is highly mobile and needs the selective substrate present to immobilize the catalytic domain.

Cys-302

In Figure 3 it is possible to see the active site, which is where the substrate interacts with Cys-302. The Cys-302 residue acts as a nucleophilic active site on each domain as a hydrogen-bond turn that is enclosed deep inside the substrate access channel. This is where the large substrate molecules can gain access to the catalytic Cys-302. The side chain of Cys-302 is the nucleophile that attaches to the substrate retinol (at its carbonyl) when it is deprotonated. To get Cys-302 deprotonated, the amino acid Glu-268 is needed as the proton acceptor.^{[5] [6]} The amine backbone of Glu-268 helps stabilize the negatively charged transition state, which helps the enzyme result in an energetically favorable conformation. Asn-187 is also used as a transition site stabilizer and is on all four domains.^{[5] [6]} It worked in a similar fashion as Glu-268, in that Asn-187 amine backbone is used to stabilize the negatively charged transition state. ^{[5] [6]}

Disease

Relevance

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References

1. ↑ ^{1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15} Lamb AL, Newcomer ME. The structure of retinal dehydrogenase type II at 2.7 A resolution: implications for retinal specificity. Biochemistry. 1999 May 11;38(19):6003-11. PMID:10320326 doi:10.1021/bi9900471
2. ↑ Ruberte E, Dolle P, Chambon P, Morriss-Kay G. Retinoic acid receptors and cellular retinoid binding proteins. II. Their differential pattern of transcription during early morphogenesis in mouse embryos. Development. 1991 Jan;111(1):45-60. PMID:1849812
3. ↑ Duester G. Families of retinoid dehydrogenases regulating vitamin A function: production of visual pigment and retinoic acid. Eur J Biochem. 2000 Jul;267(14):4315-24. PMID:10880953
4. ↑ Lamb AL, Wang X, Napoli JL, Newcomer ME. Purification, crystallization and preliminary X-ray diffraction studies of retinal dehydrogenase type II. Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):639-42. PMID:9761861
5. ↑ ^{5.0 5.1 5.2} Johansson K, El-Ahmad M, Ramaswamy S, Hjelmqvist L, Jornvall H, Eklund H. Structure of betaine aldehyde dehydrogenase at 2.1 A resolution. Protein Sci. 1998 Oct;7(10):2106-17. PMID:9792097 doi:10.1002/pro.5560071007
6. ↑ ^{6.0 6.1 6.2} Gonzalez-Segura L, Rudino-Pinera E, Munoz-Clares RA, Horjales E. The crystal structure of a ternary complex of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa Provides new insight into the reaction mechanism and shows a novel binding mode of the 2'-phosphate of NADP+ and a novel cation binding site. J Mol Biol. 2009 Jan 16;385(2):542-57. Epub 2008 Nov 5. PMID:19013472 doi:10.1016/j.jmb.2008.10.082