1f1u: Difference between revisions

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CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS (NATIVE, LOW TEMPERATURE)

OverviewOverview

The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.

About this StructureAbout this Structure

1F1U is a Single protein structure of sequence from Arthrobacter globiformis with as ligand. Active as 3,4-dihydroxyphenylacetate 2,3-dioxygenase, with EC number 1.13.11.15 Full crystallographic information is available from OCA.

ReferenceReference

Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases., Vetting MW, Wackett LP, Que L Jr, Lipscomb JD, Ohlendorf DH, J Bacteriol. 2004 Apr;186(7):1945-58. PMID:15028678

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-[[Image:1f1u.jpg|left|200px]]<br /><applet load="1f1u" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1f1u.jpg|left|200px]]<br /><applet load="1f1u" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1f1u, resolution 1.5&Aring;" />
 '''CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS (NATIVE, LOW TEMPERATURE)'''<br />
 ==Overview==
-The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases, isolated from Arthrobacter globiformis and Brevibacterium fuscum have been, determined to high resolution. These enzymes exhibit 83% sequence, identity, yet their activities depend on different transition metals, Mn2+, and Fe2+, respectively. The structures allow the origins of metal ion, selectivity and aspects of the molecular mechanism to be examined in, detail. The homotetrameric enzymes belong to the type I family of, extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer, has four betaalphabetabetabeta modules forming two structurally homologous, N-terminal and C-terminal barrel-shaped domains. The active-site metal is, located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water, molecules. The first and second coordination spheres of these enzymes are, virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a, significant distance from the metal and/or changes that occur during, folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the, metal asymmetrically at sites trans to the two imidazole ligands and, interacts with a unique, mobile C-terminal loop. The loop closes over the, bound substrate, presumably to seal the active site as the oxygen, activation process commences. An "open" coordination site trans to E267 is, the likely binding site for O2. The geometry of the enzyme-substrate, complexes suggests that if a transiently formed metal-superoxide complex, attacks the substrate without dissociation from the metal, it must do so, at the C-3 position. Second-sphere active-site residues that are, positioned to interact with the HPCA and/or bound O2 during catalysis are, identified and discussed in the context of current mechanistic hypotheses.
+The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.
 ==About this Structure==
-F1U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1F1U OCA].
+F1U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis] with <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1U OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Arthrobacter globiformis]]
 [[Category: Single protein]]
-[[Category: Jr., L.Que.]]
+[[Category: Jr., L Que.]]
-[[Category: Lipscomb, J.D.]]
+[[Category: Lipscomb, J D.]]
-[[Category: Ohlendorf, D.H.]]
+[[Category: Ohlendorf, D H.]]
-[[Category: Vetting, M.W.]]
+[[Category: Vetting, M W.]]
-[[Category: Wackett, L.P.]]
+[[Category: Wackett, L P.]]
 [[Category: MN]]
 [[Category: aromatic]]
@@ Line 26: / Line 26: @@
 [[Category: manganese]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:09:28 2007''
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