1u7h: Difference between revisions

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Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida

OverviewOverview

Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to L-proline by an NAD(+)-dependent hydride transfer reaction that culminates in ammonia elimination. Phylogenetic comparisons of amino acid sequences revealed that the enzyme belongs to the mu-crystallin protein family whose three-dimensional fold has not been reported. Here we describe the crystal structure of ornithine cyclodeaminase in complex with NADH, refined to 1.80 A resolution. The enzyme consists of a homodimeric fold whose subunits comprise two functional regions: (i) a novel substrate-binding domain whose antiparallel beta-strands form a 14-stranded barrel at the oligomeric interface and (ii) a canonical Rossmann fold that interacts with a single dinucleotide positioned for re hydride transfer. The adenosyl moiety of the cofactor resides in a solvent-exposed crevice on the protein surface and makes contact with a "domain-swapped"-like coil-helix module originating from the dyad-related molecule. Diffraction data were also collected to 1.60 A resolution on crystals grown in the presence of l-ornithine. The structure revealed that the substrate carboxyl group interacts with the side chains of Arg45, Lys69, and Arg112. In addition, the ammonia leaving group hydrogen bonds to the side chain of Asp228 and the site of hydride transfer is 3.8 A from C4 of the nicotinamide. The absence of an appropriately positioned water suggested that a previously proposed mechanism that calls for hydrolytic elimination of the imino intermediate must be reconsidered. A more parsimonious description of the chemical mechanism is proposed and discussed in relation to the structure and function of mu-crystallins.

About this StructureAbout this Structure

1U7H is a Single protein structure of sequence from Pseudomonas putida with , and as ligands. Active as Ornithine cyclodeaminase, with EC number 4.3.1.12 Full crystallographic information is available from OCA.

ReferenceReference

Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family., Goodman JL, Wang S, Alam S, Ruzicka FJ, Frey PA, Wedekind JE, Biochemistry. 2004 Nov 9;43(44):13883-91. PMID:15518536

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-[[Image:1u7h.jpg|left|200px]]<br /><applet load="1u7h" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1u7h.jpg|left|200px]]<br /><applet load="1u7h" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1u7h, resolution 1.80&Aring;" />
 '''Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida'''<br />
 ==Overview==
-Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to, L-proline by an NAD(+)-dependent hydride transfer reaction that culminates, in ammonia elimination. Phylogenetic comparisons of amino acid sequences, revealed that the enzyme belongs to the mu-crystallin protein family whose, three-dimensional fold has not been reported. Here we describe the crystal, structure of ornithine cyclodeaminase in complex with NADH, refined to, 1.80 A resolution. The enzyme consists of a homodimeric fold whose, subunits comprise two functional regions: (i) a novel substrate-binding, domain whose antiparallel beta-strands form a 14-stranded barrel at the, oligomeric interface and (ii) a canonical Rossmann fold that interacts, with a single dinucleotide positioned for re hydride transfer. The, adenosyl moiety of the cofactor resides in a solvent-exposed crevice on, the protein surface and makes contact with a "domain-swapped"-like, coil-helix module originating from the dyad-related molecule. Diffraction, data were also collected to 1.60 A resolution on crystals grown in the, presence of l-ornithine. The structure revealed that the substrate, carboxyl group interacts with the side chains of Arg45, Lys69, and Arg112., In addition, the ammonia leaving group hydrogen bonds to the side chain of, Asp228 and the site of hydride transfer is 3.8 A from C4 of the, nicotinamide. The absence of an appropriately positioned water suggested, that a previously proposed mechanism that calls for hydrolytic elimination, of the imino intermediate must be reconsidered. A more parsimonious, description of the chemical mechanism is proposed and discussed in, relation to the structure and function of mu-crystallins.
+Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to L-proline by an NAD(+)-dependent hydride transfer reaction that culminates in ammonia elimination. Phylogenetic comparisons of amino acid sequences revealed that the enzyme belongs to the mu-crystallin protein family whose three-dimensional fold has not been reported. Here we describe the crystal structure of ornithine cyclodeaminase in complex with NADH, refined to 1.80 A resolution. The enzyme consists of a homodimeric fold whose subunits comprise two functional regions: (i) a novel substrate-binding domain whose antiparallel beta-strands form a 14-stranded barrel at the oligomeric interface and (ii) a canonical Rossmann fold that interacts with a single dinucleotide positioned for re hydride transfer. The adenosyl moiety of the cofactor resides in a solvent-exposed crevice on the protein surface and makes contact with a "domain-swapped"-like coil-helix module originating from the dyad-related molecule. Diffraction data were also collected to 1.60 A resolution on crystals grown in the presence of l-ornithine. The structure revealed that the substrate carboxyl group interacts with the side chains of Arg45, Lys69, and Arg112. In addition, the ammonia leaving group hydrogen bonds to the side chain of Asp228 and the site of hydride transfer is 3.8 A from C4 of the nicotinamide. The absence of an appropriately positioned water suggested that a previously proposed mechanism that calls for hydrolytic elimination of the imino intermediate must be reconsidered. A more parsimonious description of the chemical mechanism is proposed and discussed in relation to the structure and function of mu-crystallins.
 ==About this Structure==
-U7H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with NA, NAD and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ornithine_cyclodeaminase Ornithine cyclodeaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.12 4.3.1.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1U7H OCA].
+U7H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=NAD:'>NAD</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ornithine_cyclodeaminase Ornithine cyclodeaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.12 4.3.1.12] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U7H OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Single protein]]
 [[Category: Alam, S.]]
-[[Category: Frey, P.A.]]
+[[Category: Frey, P A.]]
-[[Category: Goodman, J.L.]]
+[[Category: Goodman, J L.]]
-[[Category: Ruzicka, F.J.]]
+[[Category: Ruzicka, F J.]]
 [[Category: Wang, S.]]
-[[Category: Wedekind, J.E.]]
+[[Category: Wedekind, J E.]]
 [[Category: MPD]]
 [[Category: NA]]
@@ Line 31: / Line 31: @@
 [[Category: rossmann fold]]
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