1x7d
From Proteopedia
(New page: 200px<br /><applet load="1x7d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1x7d, resolution 1.60Å" /> '''Crystal Structure An...) |
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| - | [[Image:1x7d.jpg|left|200px]]<br /><applet load="1x7d" size=" | + | [[Image:1x7d.jpg|left|200px]]<br /><applet load="1x7d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1x7d, resolution 1.60Å" /> | caption="1x7d, resolution 1.60Å" /> | ||
'''Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms'''<br /> | '''Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to | + | 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== | ==About this Structure== | ||
| - | 1X7D 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, ORN, MES 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:// | + | 1X7D 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>, <scene name='pdbligand=ORN:'>ORN</scene>, <scene name='pdbligand=MES:'>MES</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=1X7D OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Alam, S.]] | [[Category: Alam, S.]] | ||
| - | [[Category: Frey, P | + | [[Category: Frey, P A.]] |
| - | [[Category: Goodman, J | + | [[Category: Goodman, J L.]] |
| - | [[Category: Ruzicka, F | + | [[Category: Ruzicka, F J.]] |
[[Category: Wang, S.]] | [[Category: Wang, S.]] | ||
| - | [[Category: Wedekind, J | + | [[Category: Wedekind, J E.]] |
[[Category: MES]] | [[Category: MES]] | ||
[[Category: MPD]] | [[Category: MPD]] | ||
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[[Category: rossmann fold]] | [[Category: rossmann fold]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:51:44 2008'' |
Revision as of 13:51, 21 February 2008
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Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms
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.
About this Structure
1X7D 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.
Reference
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
Page seeded by OCA on Thu Feb 21 15:51:44 2008
Categories: Ornithine cyclodeaminase | Pseudomonas putida | Single protein | Alam, S. | Frey, P A. | Goodman, J L. | Ruzicka, F J. | Wang, S. | Wedekind, J E. | MES | MPD | NA | NAD | ORN | 2 helix bundle | Beta barrel | Binds l-ornithine | Binds l-proline | Binds nad+ | Deaminase | Rossmann fold
