1egm

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(New page: 200px<br /><applet load="1egm" size="450" color="white" frame="true" align="right" spinBox="true" caption="1egm, resolution 1.85&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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'''CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K.'''<br />
'''CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K.'''<br />
==Overview==
==Overview==
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BACKGROUND: Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for, enzymatic radical reactions. The adenosyl radical, a catalytic radical in, these reactions, is formed by homolysis of the cobalt-carbon bond of the, coenzyme, although the mechanism of cleavage of its organometallic bond, remains unsolved. RESULTS: We determined the three-dimensional structures, of diol dehydratase complexed with adeninylpentylcobalamin and with, cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic, temperatures. In the adeninylpentylcobalamin complex, the adenine ring is, bound parallel to the corrin ring as in the free form and, methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing, pyrrole ring C. All of its nitrogen atoms except for N(9) are, hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a, sidechain hydroxyl group, and a water molecule. As compared with the, cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120, degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS: The, structure of the adenine-ring-binding site provides a molecular basis for, the strict specificity of diol dehydratase for the coenzyme adenosyl, group. The superimposition of the structure of the free coenzyme on that, of enzyme-bound adeninylpentylcobalamin demonstrated that the tight, enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring, of the adenosyl group would inevitably lead to cleavage of the, cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic, linkage makes the 5'-carbon radical accessible to the hydrogen atom of the, substrate to be abstracted.
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BACKGROUND: Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved. RESULTS: We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS: The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.
==About this Structure==
==About this Structure==
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1EGM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca] with K, CNC and PGO as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EGM OCA].
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1EGM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca] with <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=CNC:'>CNC</scene> and <scene name='pdbligand=PGO:'>PGO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EGM OCA].
==Reference==
==Reference==
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[[Category: tim barrel]]
[[Category: tim barrel]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:13:24 2007''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:27:31 2008''

Revision as of 10:27, 21 February 2008

Image:1egm.jpg

1egm, resolution 1.85Å

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CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K.

Overview

BACKGROUND: Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved. RESULTS: We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS: The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.

About this Structure

1EGM is a Protein complex structure of sequences from Klebsiella oxytoca with , and as ligands. Active as Propanediol dehydratase, with EC number 4.2.1.28 Full crystallographic information is available from OCA.

Reference

How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex., Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N, Structure. 2000 Jul 15;8(7):775-88. PMID:10903944

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