2ihp: Difference between revisions

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Yeast inorganic pyrophosphatase with magnesium and phosphate

OverviewOverview

We have determined the structures of the wild type and seven active site variants of yeast inorganic pyrophosphatase (PPase) in the presence of Mg2+ and phosphate, providing the first complete structural description of its catalytic cycle. PPases catalyze the hydrolysis of pyrophosphate and require four divalent metal cations for catalysis; magnesium provides the highest activity. The crystal form chosen contains two monomers in the asymmetric unit, corresponding to distinct catalytic intermediates. In the "closed" wild-type active site, one of the two product phosphates has already dissociated, while the D115E variant "open" conformation is of the hitherto unobserved two-phosphate and two-"bridging" water active site. The mutations affect metal binding and the hydrogen bonding network in the active site, allowing us to explain the effects of mutations. For instance, in Y93F, F93 binds in a cryptic hydrophobic pocket in the absence of substrate, preserving hydrogen bonding in the active site and leading to relatively small changes in solution properties. This is not true in the presence of substrate, when F93 is forced back into the active site. Such subtle changes underline how low the energy barriers are between thermodynamically favorable conformations of the enzyme. The structures also allow us to associate metal binding constants to specific sites. Finally, the wild type and the D152E variant contain a phosphate ion adjacent to the active site, showing for the first time how product is released through a channel of flexible cationic side chains.

About this StructureAbout this Structure

2IHP is a Single protein structure of sequence from Saccharomyces cerevisiae with , and as ligands. Active as Inorganic diphosphatase, with EC number 3.6.1.1 Full crystallographic information is available from OCA.

ReferenceReference

A complete structural description of the catalytic cycle of yeast pyrophosphatase., Oksanen E, Ahonen AK, Tuominen H, Tuominen V, Lahti R, Goldman A, Heikinheimo P, Biochemistry. 2007 Feb 6;46(5):1228-39. PMID:17260952

Page seeded by OCA on Thu Feb 21 17:52:47 2008

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OCA

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-[[Image:2ihp.jpg|left|200px]]<br /><applet load="2ihp" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2ihp.jpg|left|200px]]<br /><applet load="2ihp" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2ihp, resolution 1.500&Aring;" />
 '''Yeast inorganic pyrophosphatase with magnesium and phosphate'''<br />
 ==Overview==
-We have determined the structures of the wild type and seven active site, variants of yeast inorganic pyrophosphatase (PPase) in the presence of, Mg2+ and phosphate, providing the first complete structural description of, its catalytic cycle. PPases catalyze the hydrolysis of pyrophosphate and, require four divalent metal cations for catalysis; magnesium provides the, highest activity. The crystal form chosen contains two monomers in the, asymmetric unit, corresponding to distinct catalytic intermediates. In the, "closed" wild-type active site, one of the two product phosphates has, already dissociated, while the D115E variant "open" conformation is of the, hitherto unobserved two-phosphate and two-"bridging" water active site., The mutations affect metal binding and the hydrogen bonding network in the, active site, allowing us to explain the effects of mutations. For, instance, in Y93F, F93 binds in a cryptic hydrophobic pocket in the, absence of substrate, preserving hydrogen bonding in the active site and, leading to relatively small changes in solution properties. This is not, true in the presence of substrate, when F93 is forced back into the active, site. Such subtle changes underline how low the energy barriers are, between thermodynamically favorable conformations of the enzyme. The, structures also allow us to associate metal binding constants to specific, sites. Finally, the wild type and the D152E variant contain a phosphate, ion adjacent to the active site, showing for the first time how product is, released through a channel of flexible cationic side chains.
+We have determined the structures of the wild type and seven active site variants of yeast inorganic pyrophosphatase (PPase) in the presence of Mg2+ and phosphate, providing the first complete structural description of its catalytic cycle. PPases catalyze the hydrolysis of pyrophosphate and require four divalent metal cations for catalysis; magnesium provides the highest activity. The crystal form chosen contains two monomers in the asymmetric unit, corresponding to distinct catalytic intermediates. In the "closed" wild-type active site, one of the two product phosphates has already dissociated, while the D115E variant "open" conformation is of the hitherto unobserved two-phosphate and two-"bridging" water active site. The mutations affect metal binding and the hydrogen bonding network in the active site, allowing us to explain the effects of mutations. For instance, in Y93F, F93 binds in a cryptic hydrophobic pocket in the absence of substrate, preserving hydrogen bonding in the active site and leading to relatively small changes in solution properties. This is not true in the presence of substrate, when F93 is forced back into the active site. Such subtle changes underline how low the energy barriers are between thermodynamically favorable conformations of the enzyme. The structures also allow us to associate metal binding constants to specific sites. Finally, the wild type and the D152E variant contain a phosphate ion adjacent to the active site, showing for the first time how product is released through a channel of flexible cationic side chains.
 ==About this Structure==
-IHP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MG, PO4 and MES as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IHP OCA].
+IHP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=MES:'>MES</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IHP OCA].
 ==Reference==
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 [[Category: Saccharomyces cerevisiae]]
 [[Category: Single protein]]
-[[Category: Ahonen, A.K.]]
+[[Category: Ahonen, A K.]]
 [[Category: Goldman, A.]]
 [[Category: Heikinheimo, P.]]
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 [[Category: x-ray crystallography]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:19:27 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:52:47 2008''