1evi
From Proteopedia
(New page: 200px<br /><applet load="1evi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1evi, resolution 2.5Å" /> '''THREE-DIMENSIONAL STR...) |
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| - | [[Image:1evi.gif|left|200px]]<br /><applet load="1evi" size=" | + | [[Image:1evi.gif|left|200px]]<br /><applet load="1evi" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1evi, resolution 2.5Å" /> | caption="1evi, resolution 2.5Å" /> | ||
'''THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE'''<br /> | '''THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional structure of the purple intermediate of porcine | + | The three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase (DAO) was solved by cryo-X-ray crystallography; the purple intermediate is known to comprise a complex between the dehydrogenated product, an imino acid, and the reduced form of DAO. The crystalline purple intermediate was obtained by anaerobically soaking crystals of oxidized DAO in a buffer containing excess D-proline as the substrate. The dehydrogenated product, delta(1)-pyrrolidine-2-carboxylate (DPC), is found sandwiched between the phenol ring of Tyr 224 and the planar reduced flavin ring. The cationic protonated imino nitrogen is within hydrogen-bonding distance of the backbone carbonyl oxygen of Gly 313. The carboxyl group of DPC is recognized by the Arg 283 guanidino and Tyr 228 hydroxyl groups through ion-pairing and hydrogen-bonding, respectively. The (+)HN=C double bond of DPC overlaps the N(5)-C(4a) bond of reduced flavin. The electrostatic effect of the cationic nitrogen of DPC is suggested to shift the resonance hybridization of anionic reduced flavin toward a canonical form with a negative charge at C(4a), thereby augmenting the electron density at C(4a), from which electrons are transferred to molecular oxygen during reoxidation of reduced flavin. The reactivity of reduced flavin in the purple intermediate, therefore, is enhanced through the alignment of DPC with respect to reduced flavin. |
==About this Structure== | ==About this Structure== | ||
| - | 1EVI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with FAD and 2PC as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] Full crystallographic information is available from [http:// | + | 1EVI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with <scene name='pdbligand=FAD:'>FAD</scene> and <scene name='pdbligand=2PC:'>2PC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVI OCA]. |
==Reference== | ==Reference== | ||
| - | Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin., Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R, J Biochem | + | Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin., Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R, J Biochem. 2000 Jul;128(1):73-81. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10876160 10876160] |
[[Category: D-amino-acid oxidase]] | [[Category: D-amino-acid oxidase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: flavoenzyme]] | [[Category: flavoenzyme]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:31:59 2008'' |
Revision as of 10:32, 21 February 2008
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THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE
Overview
The three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase (DAO) was solved by cryo-X-ray crystallography; the purple intermediate is known to comprise a complex between the dehydrogenated product, an imino acid, and the reduced form of DAO. The crystalline purple intermediate was obtained by anaerobically soaking crystals of oxidized DAO in a buffer containing excess D-proline as the substrate. The dehydrogenated product, delta(1)-pyrrolidine-2-carboxylate (DPC), is found sandwiched between the phenol ring of Tyr 224 and the planar reduced flavin ring. The cationic protonated imino nitrogen is within hydrogen-bonding distance of the backbone carbonyl oxygen of Gly 313. The carboxyl group of DPC is recognized by the Arg 283 guanidino and Tyr 228 hydroxyl groups through ion-pairing and hydrogen-bonding, respectively. The (+)HN=C double bond of DPC overlaps the N(5)-C(4a) bond of reduced flavin. The electrostatic effect of the cationic nitrogen of DPC is suggested to shift the resonance hybridization of anionic reduced flavin toward a canonical form with a negative charge at C(4a), thereby augmenting the electron density at C(4a), from which electrons are transferred to molecular oxygen during reoxidation of reduced flavin. The reactivity of reduced flavin in the purple intermediate, therefore, is enhanced through the alignment of DPC with respect to reduced flavin.
About this Structure
1EVI is a Single protein structure of sequence from Sus scrofa with and as ligands. Active as D-amino-acid oxidase, with EC number 1.4.3.3 Full crystallographic information is available from OCA.
Reference
Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin., Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R, J Biochem. 2000 Jul;128(1):73-81. PMID:10876160
Page seeded by OCA on Thu Feb 21 12:31:59 2008
Categories: D-amino-acid oxidase | Single protein | Sus scrofa | Hirotsu, K. | Miura, R. | Miyahara, I. | Mizutani, H. | Nishina, Y. | Setoyama, C. | Shiga, K. | 2PC | FAD | Flavoenzyme
