1eoc: Difference between revisions
New page: left|200px<br /><applet load="1eoc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1eoc, resolution 2.25Å" /> '''CRYSTAL STRUCTURE OF... |
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[[Image:1eoc.gif|left|200px]]<br /><applet load="1eoc" size=" | [[Image:1eoc.gif|left|200px]]<br /><applet load="1eoc" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1eoc, resolution 2.25Å" /> | caption="1eoc, resolution 2.25Å" /> | ||
'''CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 4-NITROCATECHOL'''<br /> | '''CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 4-NITROCATECHOL'''<br /> | ||
==Overview== | ==Overview== | ||
The crystal structures of protocatechuate 3,4-dioxygenase from the soil | The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases. The overall tertiary and quaternary structures of Ac 3,4-PCD are similar to those of the same enzyme from Pseudomonas putida[Ohlendorf et al. (1994) J. Mol. Biol. 244, 586-608]. At pH 8.5, the catalytic non-heme Fe(3+) is coordinated by two axial ligands, Tyr447(OH) (147beta) and His460(N)(epsilon)(2) (160beta), and three equatorial ligands, Tyr408(OH) (108beta), His462(N)(epsilon)(2) (162beta), and a hydroxide ion (d(Fe-OH) = 1.91 A) in a distorted bipyramidal geometry. At pH 5.75, difference maps suggest a sulfate binds to the Fe(3+) in an equatorial position and the hydroxide is shifted [d(Fe-OH) = 2.3 A] yielding octahedral geometry for the active site Fe(3+). This change in ligation geometry is concomitant with a shift in the optical absorbance spectrum of the enzyme from lambda(max) = 450 nm to lambda(max) = 520 nm. Binding of substrate or 4-NC to the Fe(3+) is bidentate with the axial ligand Tyr447(OH) (147beta) dissociating. The structure of the 4-NC complex supports the view that resonance delocalization of the positive character of the nitrogen prevents substrate activation. The cyanide complex confirms previous work that protocatechuate 3,4-dioxygenases have three coordination sites available for binding by exogenous substrates. A significant conformational change extending away from the active site is seen in all structures when compared to the native enzyme at pH 8.5. This conformational change is discussed in its relevance to enhancing catalysis in protocatechuate 3,4-dioxygenases. | ||
==About this Structure== | ==About this Structure== | ||
1EOC is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.] with FE and 4NC as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] Full crystallographic information is available from [http:// | 1EOC is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=4NC:'>4NC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EOC OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Protocatechuate 3,4-dioxygenase]] | [[Category: Protocatechuate 3,4-dioxygenase]] | ||
[[Category: Argenio, D | [[Category: Argenio, D A.D.]] | ||
[[Category: Ohlendorf, D | [[Category: Ohlendorf, D H.]] | ||
[[Category: Ornston, L | [[Category: Ornston, L N.]] | ||
[[Category: Vetting, M | [[Category: Vetting, M W.]] | ||
[[Category: 4NC]] | [[Category: 4NC]] | ||
[[Category: FE]] | [[Category: FE]] | ||
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[[Category: mixed alpha/beta structure]] | [[Category: mixed alpha/beta structure]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:29:55 2008'' | ||
Revision as of 13:29, 21 February 2008
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CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 4-NITROCATECHOL
OverviewOverview
The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases. The overall tertiary and quaternary structures of Ac 3,4-PCD are similar to those of the same enzyme from Pseudomonas putida[Ohlendorf et al. (1994) J. Mol. Biol. 244, 586-608]. At pH 8.5, the catalytic non-heme Fe(3+) is coordinated by two axial ligands, Tyr447(OH) (147beta) and His460(N)(epsilon)(2) (160beta), and three equatorial ligands, Tyr408(OH) (108beta), His462(N)(epsilon)(2) (162beta), and a hydroxide ion (d(Fe-OH) = 1.91 A) in a distorted bipyramidal geometry. At pH 5.75, difference maps suggest a sulfate binds to the Fe(3+) in an equatorial position and the hydroxide is shifted [d(Fe-OH) = 2.3 A] yielding octahedral geometry for the active site Fe(3+). This change in ligation geometry is concomitant with a shift in the optical absorbance spectrum of the enzyme from lambda(max) = 450 nm to lambda(max) = 520 nm. Binding of substrate or 4-NC to the Fe(3+) is bidentate with the axial ligand Tyr447(OH) (147beta) dissociating. The structure of the 4-NC complex supports the view that resonance delocalization of the positive character of the nitrogen prevents substrate activation. The cyanide complex confirms previous work that protocatechuate 3,4-dioxygenases have three coordination sites available for binding by exogenous substrates. A significant conformational change extending away from the active site is seen in all structures when compared to the native enzyme at pH 8.5. This conformational change is discussed in its relevance to enhancing catalysis in protocatechuate 3,4-dioxygenases.
About this StructureAbout this Structure
1EOC is a Protein complex structure of sequences from Acinetobacter sp. with and as ligands. Active as Protocatechuate 3,4-dioxygenase, with EC number 1.13.11.3 Full crystallographic information is available from OCA.
ReferenceReference
Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase., Vetting MW, D'Argenio DA, Ornston LN, Ohlendorf DH, Biochemistry. 2000 Jul 11;39(27):7943-55. PMID:10891075
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