1siq: Difference between revisions
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'''The Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydrogenase''' | {{Structure | ||
|PDB= 1siq |SIZE=350|CAPTION= <scene name='initialview01'>1siq</scene>, resolution 2.10Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=FAD:FLAVIN-ADENINE DINUCLEOTIDE'>FAD</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Glutaryl-CoA_dehydrogenase Glutaryl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.7 1.3.99.7] | |||
|GENE= | |||
}} | |||
'''The Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydrogenase''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1SIQ is a [ | 1SIQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SIQ OCA]. | ||
==Reference== | ==Reference== | ||
Crystal structures of human glutaryl-CoA dehydrogenase with and without an alternate substrate: structural bases of dehydrogenation and decarboxylation reactions., Fu Z, Wang M, Paschke R, Rao KS, Frerman FE, Kim JJ, Biochemistry. 2004 Aug 3;43(30):9674-84. PMID:[http:// | Crystal structures of human glutaryl-CoA dehydrogenase with and without an alternate substrate: structural bases of dehydrogenation and decarboxylation reactions., Fu Z, Wang M, Paschke R, Rao KS, Frerman FE, Kim JJ, Biochemistry. 2004 Aug 3;43(30):9674-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15274622 15274622] | ||
[[Category: Glutaryl-CoA dehydrogenase]] | [[Category: Glutaryl-CoA dehydrogenase]] | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
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[[Category: flavin protein]] | [[Category: flavin protein]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:05:25 2008'' | ||
Revision as of 15:05, 20 March 2008
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| , resolution 2.10Å | |||||||
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| Ligands: | |||||||
| Activity: | Glutaryl-CoA dehydrogenase, with EC number 1.3.99.7 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydrogenase
OverviewOverview
Acyl-CoA dehydrogenases (ACDs) are a family of flavoenzymes that metabolize fatty acids and some amino acids. Of nine known ACDs, glutaryl-CoA dehydrogenase (GCD) is unique: in addition to the alpha,beta-dehydrogenation reaction, common to all ACDs, GCD catalyzes decarboxylation of glutaryl-CoA to produce CO(2) and crotonyl-CoA. Crystal structures of GCD and its complex with 4-nitrobutyryl-CoA have been determined to 2.1 and 2.6 A, respectively. The overall polypeptide folds are the same and similar to the structures of other family members. The active site of the unliganded structure is filled with water molecules that are displaced when enzyme binds the substrate. The structure strongly suggests that the mechanism of dehydrogenation is the same as in other ACDs. The substrate binds at the re side of the FAD ring. Glu370 abstracts the C2 pro-R proton, which is acidified by the polarization of the thiolester carbonyl oxygen through hydrogen bonding to the 2'-OH of FAD and the amide nitrogen of Glu370. The C3 pro-R proton is transferred to the N(5) atom of FAD. The structures indicate a plausible mechanism for the decarboxylation reaction. The carbonyl polarization initiates decarboxylation, and Arg94 stabilizes the transient crotonyl-CoA anion. Protonation of the crotonyl-CoA anion occurs by a 1,3-prototropic shift catalyzed by the conjugated acid of the general base, Glu370. A tight hydrogen-bonding network involving gamma-carboxylate of the enzyme-bound glutaconyl-CoA, with Tyr369, Glu87, Arg94, Ser95, and Thr170, optimizes orientation of the gamma-carboxylate for decarboxylation. Some pathogenic mutations are explained by the structure. The mutations affect protein folding, stability, and/or substrate binding, resulting in inefficient/inactive enzyme.
DiseaseDisease
Known disease associated with this structure: Glutaricaciduria, type I OMIM:[608801]
About this StructureAbout this Structure
1SIQ is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structures of human glutaryl-CoA dehydrogenase with and without an alternate substrate: structural bases of dehydrogenation and decarboxylation reactions., Fu Z, Wang M, Paschke R, Rao KS, Frerman FE, Kim JJ, Biochemistry. 2004 Aug 3;43(30):9674-84. PMID:15274622
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