2ofx
From Proteopedia
(New page: 200px<br /> <applet load="2ofx" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ofx, resolution 1.900Å" /> '''crystal structure ...) |
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| - | [[Image:2ofx.gif|left|200px]]<br /> | + | [[Image:2ofx.gif|left|200px]]<br /><applet load="2ofx" size="350" color="white" frame="true" align="right" spinBox="true" |
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caption="2ofx, resolution 1.900Å" /> | caption="2ofx, resolution 1.900Å" /> | ||
'''crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS'''<br /> | '''crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Bifunctional human PAPS synthetase (PAPSS) catalyzes, in a two-step | + | Bifunctional human PAPS synthetase (PAPSS) catalyzes, in a two-step process, the formation of the activated sulfate carrier 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The first reaction involves the formation of the 5'-adenosine phosphosulfate (APS) intermediate from ATP and inorganic sulfate. APS is then further phosphorylated on its 3'-hydroxyl group by an additional ATP molecule to generate PAPS. The former reaction is catalyzed by the ATP-sulfurylase domain and the latter by the APS-kinase domain. Here, we report the structure of the APS-kinase domain of PAPSS isoform 1 (PAPSS1) representing the Michaelis complex with the products ADP-Mg and PAPS. This structure provides a rare glimpse of the active conformation of an enzyme catalyzing phosphoryl transfer without resorting to substrate analogs, inactivating mutations, or catalytically non-competent conditions. Our structure shows the interactions involved in the binding of the magnesium ion and PAPS, thereby revealing residues critical for catalysis. The essential magnesium ion is observed bridging the phosphate groups of the products. This function of the metal ion is made possible by the DGDN-loop changing its conformation from that previously reported, and identifies these loop residues unambiguously as a Walker B motif. Furthermore, the second aspartate residue of this motif is the likely candidate for initiating nucleophilic attack on the ATP gamma-phosphate group by abstracting the proton from the 3'-hydroxyl group of the substrate APS. We report the structure of the APS-kinase domain of human PAPSS1 in complex with two APS molecules, demonstrating the ability of the ATP/ADP-binding site to bind APS. Both structures reveal extended N termini that approach the active site of the neighboring monomer. Together, these results significantly increase our understandings of how catalysis is achieved by APS-kinase. |
==Disease== | ==Disease== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2OFX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MG, PO4, PPS and ADP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Adenylyl-sulfate_kinase Adenylyl-sulfate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.25 2.7.1.25] Full crystallographic information is available from [http:// | + | 2OFX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=PPS:'>PPS</scene> and <scene name='pdbligand=ADP:'>ADP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Adenylyl-sulfate_kinase Adenylyl-sulfate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.25 2.7.1.25] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OFX OCA]. |
==Reference== | ==Reference== | ||
| - | Elucidation of the | + | Elucidation of the active conformation of the APS-kinase domain of human PAPS synthetase 1., Sekulic N, Dietrich K, Paarmann I, Ort S, Konrad M, Lavie A, J Mol Biol. 2007 Mar 23;367(2):488-500. Epub 2007 Jan 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17276460 17276460] |
[[Category: Adenylyl-sulfate kinase]] | [[Category: Adenylyl-sulfate kinase]] | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
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[[Category: nucleotide kinase]] | [[Category: nucleotide kinase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:18:03 2008'' |
Revision as of 16:18, 21 February 2008
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crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS
Contents |
Overview
Bifunctional human PAPS synthetase (PAPSS) catalyzes, in a two-step process, the formation of the activated sulfate carrier 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The first reaction involves the formation of the 5'-adenosine phosphosulfate (APS) intermediate from ATP and inorganic sulfate. APS is then further phosphorylated on its 3'-hydroxyl group by an additional ATP molecule to generate PAPS. The former reaction is catalyzed by the ATP-sulfurylase domain and the latter by the APS-kinase domain. Here, we report the structure of the APS-kinase domain of PAPSS isoform 1 (PAPSS1) representing the Michaelis complex with the products ADP-Mg and PAPS. This structure provides a rare glimpse of the active conformation of an enzyme catalyzing phosphoryl transfer without resorting to substrate analogs, inactivating mutations, or catalytically non-competent conditions. Our structure shows the interactions involved in the binding of the magnesium ion and PAPS, thereby revealing residues critical for catalysis. The essential magnesium ion is observed bridging the phosphate groups of the products. This function of the metal ion is made possible by the DGDN-loop changing its conformation from that previously reported, and identifies these loop residues unambiguously as a Walker B motif. Furthermore, the second aspartate residue of this motif is the likely candidate for initiating nucleophilic attack on the ATP gamma-phosphate group by abstracting the proton from the 3'-hydroxyl group of the substrate APS. We report the structure of the APS-kinase domain of human PAPSS1 in complex with two APS molecules, demonstrating the ability of the ATP/ADP-binding site to bind APS. Both structures reveal extended N termini that approach the active site of the neighboring monomer. Together, these results significantly increase our understandings of how catalysis is achieved by APS-kinase.
Disease
Known disease associated with this structure: SEMD, Pakistani type OMIM:[603005]
About this Structure
2OFX is a Single protein structure of sequence from Homo sapiens with , , and as ligands. Active as Adenylyl-sulfate kinase, with EC number 2.7.1.25 Full crystallographic information is available from OCA.
Reference
Elucidation of the active conformation of the APS-kinase domain of human PAPS synthetase 1., Sekulic N, Dietrich K, Paarmann I, Ort S, Konrad M, Lavie A, J Mol Biol. 2007 Mar 23;367(2):488-500. Epub 2007 Jan 12. PMID:17276460
Page seeded by OCA on Thu Feb 21 18:18:03 2008
Categories: Adenylyl-sulfate kinase | Homo sapiens | Single protein | Lavie, A. | Sekulic, N. | ADP | MG | PO4 | PPS | Nucleotide kinase
