Sandbox Reserved 1475: Difference between revisions

Line 9:

This molecular structure is Retinal Dehydrogenase Type Two (RalDH2) which was extracted from ''Rattus norvegicus''.<ref name="Lamb AL, Newcomber ME">PMID:10320326</ref> This enzyme is part of the super family Aldehyde Dehydrogenase. The sample was a crystallization of a clone of RalDH2 that was given as a gift from J. L. Napoli. It has been shown that RalDH2, the cellular binding protein type I, and the retinol binding protein receptor all co-localize in tissues that require Vitamin A (retinol) for normal development in rat embryos post-gastrulation, as discussed by "personal communication" to the authors of the ''"The Structure of Retinal Dehydrogenase Type II at 2.7 Angstrom Resolution: Implications for Retinal Specificity"''.<ref name="Lamb AL, Newcomber ME" /> RalDH2 is the enzyme that produces retinoic acid in mouse embryos during gastrulation, and is found to be surrounding the primitive node, which is where retinal is converted into retinoic acid.<ref name ="Ruberte E">PMID:1849812</ref>

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.<ref name="Lamb AL, Newcomber ME" /> This is the last step in the formation of the hormone from Vitamin A (retinol).<ref name="Lamb AL, Newcomber ME" /> Vitamin A that has been metabolized can produce retinoid derivatives which function in either vision or growth and development. <ref name ="Families of Retinoic Dehydrogenases" /> RalDH2 is expressed in ''Escherichia coli'' strain BL21(DE3) <ref name=Lamb Al, Wang X>PMID:9761861</ref>

== Function ==

The reaction of this enzyme is [(retinal) + (NAD+) + (H2O) ↔ (retinoic acid) + (NADH) + (H+)].

The main function of this enzyme is to Retinoic acid. RalDH2 requires (NAD+) as a cofactor.<ref name="Lamb AL, Newcomber ME" /> 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.<ref name="Lamb AL, Newcomber ME" /> 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.

The main function of this enzyme is to produce Retinoic acid. RalDH2 requires (NAD+) as a cofactor.<ref name="Lamb AL, Newcomber ME" /> In the oxidoreductase reaction, NAD+ acts as an electron acceptor. 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.<ref name="Lamb AL, Newcomber ME" /> 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

Line 23:

Line 24:

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" />

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]].<ref name="Lamb AL, Newcomber ME" /> In [[Figure 3]] it is possible to see the active site, which is where the substrate interacts with Cys-302.

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]].<ref name="Lamb AL, Newcomber ME" /> The <scene name='80/800654/1st_dimerization/1'>1st dimerization</scene> 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.<ref name="Lamb AL, Newcomber ME" />

In [[Figure 3]] it is possible to see the active site, which is where the substrate interacts with Cys-302.

</StructureSection>

===Cofactor NAD and Cl ions===

The crystal structure was cocrystallized with <scene name='80/800654/Nad/1'>NAD</scene>, and was determined at a 2.7 Angstrom resolution. <ref name="Lamb AL, Newcomber ME" /> 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.<ref name="Lamb AL, Newcomber ME" /> The Chloride ions participate in hydrophobic interactions with Arg which also help maintain the folded structure.<ref name="Lamb AL, Newcomber ME" />

===

===~~Substrate NAD===~~

~~The crystal structure was cocrystallized with <scene name='80/800654/Nad/1'>NAD</scene>, and was determined at a 2.7 Angstrom resolution. <ref name="Lamb AL, Newcomber ME" />~~

Sandbox Reserved 1475: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 9: / Line 9: @@
 This molecular structure is Retinal Dehydrogenase Type Two (RalDH2) which was extracted from ''Rattus norvegicus''.<ref name="Lamb AL, Newcomber ME">PMID:10320326</ref> This enzyme is part of the super family Aldehyde Dehydrogenase. The sample was a crystallization of a clone of RalDH2 that was  given as a gift from J. L. Napoli. It has been shown that RalDH2, the cellular binding protein type I, and the retinol binding protein receptor all co-localize in tissues that require Vitamin A (retinol) for normal development in rat embryos post-gastrulation, as discussed by "personal communication" to the authors of the ''"The Structure of Retinal Dehydrogenase Type II at 2.7 Angstrom Resolution: Implications for Retinal Specificity"''.<ref name="Lamb AL, Newcomber ME" /> RalDH2 is the enzyme that produces retinoic acid in mouse embryos during gastrulation, and is found to be surrounding the primitive node, which is where retinal is converted into retinoic acid.<ref name ="Ruberte E">PMID:1849812</ref>
 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.<ref name="Lamb AL, Newcomber ME" /> This is the last step in the formation of the hormone from Vitamin A (retinol).<ref name="Lamb AL, Newcomber ME" /> Vitamin A that has been metabolized can produce retinoid derivatives which function in either vision or growth and development. <ref name ="Families of Retinoic Dehydrogenases" /> RalDH2 is expressed in ''Escherichia coli'' strain BL21(DE3) <ref name=Lamb Al, Wang X>PMID:9761861</ref>
 == Function ==
+The reaction of this enzyme is [(retinal) + (NAD+) + (H2O) ↔ (retinoic acid) + (NADH) + (H+)].
-The main function of this enzyme is to Retinoic acid. RalDH2 requires (NAD+) as a cofactor.<ref name="Lamb AL, Newcomber ME" /> 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.<ref name="Lamb AL, Newcomber ME" /> 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.
+The main function of this enzyme is to produce Retinoic acid. RalDH2 requires (NAD+) as a cofactor.<ref name="Lamb AL, Newcomber ME" /> In the oxidoreductase reaction, NAD+ acts as an electron acceptor. 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.<ref name="Lamb AL, Newcomber ME" /> 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
@@ Line 23: / Line 24: @@
 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" />
-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]].<ref name="Lamb AL, Newcomber ME" />  In [[Figure 3]] it is possible to see the active site, which is where the substrate interacts with Cys-302.
+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]].<ref name="Lamb AL, Newcomber ME" />  The <scene name='80/800654/1st_dimerization/1'>1st dimerization</scene> 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.<ref name="Lamb AL, Newcomber ME" />
+In [[Figure 3]] it is possible to see the active site, which is where the substrate interacts with Cys-302.
 </StructureSection>
+===Cofactor NAD and Cl ions===
+The crystal structure was cocrystallized with <scene name='80/800654/Nad/1'>NAD</scene>, and was determined at a 2.7 Angstrom resolution. <ref name="Lamb AL, Newcomber ME" /> 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.<ref name="Lamb AL, Newcomber ME" />  The Chloride ions participate in hydrophobic interactions with Arg which also help maintain the folded structure.<ref name="Lamb AL, Newcomber ME" />
+===
-===Substrate NAD===
-The crystal structure was cocrystallized with <scene name='80/800654/Nad/1'>NAD</scene>, and was determined at a 2.7 Angstrom resolution. <ref name="Lamb AL, Newcomber ME" />