Sandbox Reserved 1475

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== Structural highlights ==
== Structural highlights ==
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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).<ref name="Lamb AL, Newcomber ME" /> [[Image:3 Domains of RalDH2.png|thumb|Nucleotide-binding domain - orange, Catalytic domain - green, Tetramerization domain - blue. Imagine modified in Chimera from (PDB entry [[1bi9]]). Chain D shown with NAD substrate shown in pink]]
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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.<ref name="Lamb AL, Newcomber ME" /> [[Image:3 Domains of RalDH2.png|thumb|upright=2| '''Figure 1''' Nucleotide-binding domain - orange, Catalytic domain - green, Tetramerization domain - blue. Imagine modified in Chimera from (PDB entry [[1bi9]]). Chain D shown with NAD substrate shown in pink]]
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Revision as of 04:23, 7 December 2018

</StructureSection>

This Sandbox is Reserved from November 5 2018 through January 1, 2019 for use in the course "CHEM 4923: Senior Project taught by Christina R. Bourne at the University of Oklahoma, Norman, USA. This reservation includes Sandbox Reserved 1471 through Sandbox Reserved 1478.
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Contents

Retinal Dehydrogenase Type Two Structure

Retinal Dehydrogenase Type Two with NAD bound (PDB entry 1bi9)

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This molecular structure is Retinal Dehydrogenase Type Two (RalDH2). This enzyme is part of the super family Aldehyde Dehydrogenase. The function of this enzyme is to catalyze the oxidation of retinal to retinoic acid. Retinoic acid produces a putative morphogen that initiates pattern formation in the early embryo.[1] This is the last step in the formation of the hormone from Vitamin A (retinol).[1] Vitamin A that has been metabolized can produce retinoid derivatives which function in either vision or growth and development. [2] RalDH2 is expressed in Escherichia coli strain BL21(DE3) [3]

Function

The main function of this enzyme is to Retinoic acid. RalDH2 requires (NAD+) as a cofactor.[1] In the oxidoreductase reaction, NAD+ acts as an electron acceptor. The reaction of this enzyme is [(retinal) + (NAD+) + (H2O) ↔ (retinoic acid) + (NADH) + (H+) ]. Once the NAD+ is bound, hydrogen bonds form with non-polar residues and one basic Lysine residue. Chloride ions participate in hydrophobic interactions with Arginine residues.[1] Theres interactions cause a structural change to occur in the RalDH2 enzyme which causes it to form a more favorable folded confirmation. In the enzyme a large binding cavity is formed. tructural changes occur to stabilize the tertiary structure of RalDH2

Disease

Relevance

Structural highlights

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]
Figure 1 Nucleotide-binding domain - orange, Catalytic domain - green, Tetramerization domain - blue. Imagine modified in Chimera from (PDB entry 1bi9). Chain D shown with NAD substrate shown in pink
Figure 1 Nucleotide-binding domain - orange, Catalytic domain - green, Tetramerization domain - blue. Imagine modified in Chimera from (PDB entry 1bi9). Chain D shown with NAD substrate shown in pink







Substrate NAD

The crystal structure was cocrystallized with , and was determined at a 2.7 Angstrom resolution. [1]


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References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 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. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named Families_of_Retinoic_Dehydrogenases
  3. ↑ 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
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