1s3n: Difference between revisions

Revision as of 15:57, 21 February 2008

Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase

OverviewOverview

Methanococcus jannaschii MJ0936 is a hypothetical protein of unknown function with over 50 homologs found in many bacteria and Archaea. To help define the molecular (biochemical and biophysical) function of MJ0936, we determined its crystal structure at 2.4-A resolution and performed a series of biochemical screens for catalytic activity. The overall fold of this single domain protein consists of a four-layered structure formed by two beta-sheets flanked by alpha-helices on both sides. The crystal structure suggested its biochemical function to be a nuclease, phosphatase, or nucleotidase, with a requirement for some metal ions. Crystallization in the presence of Ni(2+) or Mn(2+) produced a protein containing a binuclear metal center in the putative active site formed by a cluster of conserved residues. Analysis of MJ0936 against a panel of general enzymatic assays revealed catalytic activity toward bis-p-nitrophenyl phosphate, an indicator substrate for phosphodiesterases and nucleases. Significant activity was also found with two other phosphodiesterase substrates, thymidine 5'-monophosphate p-nitrophenyl ester and p-nitrophenylphosphorylcholine, but no activity was found for cAMP or cGMP. Phosphodiesterase activity of MJ0936 had an absolute requirement for divalent metal ions with Ni(2+) and Mn(2+) being most effective. Thus, our structural and enzymatic studies have identified the biochemical function of MJ0936 as that of a novel phosphodiesterase.

About this StructureAbout this Structure

1S3N is a Single protein structure of sequence from Methanocaldococcus jannaschii with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii., Chen S, Yakunin AF, Kuznetsova E, Busso D, Pufan R, Proudfoot M, Kim R, Kim SH, J Biol Chem. 2004 Jul 23;279(30):31854-62. Epub 2004 May 5. PMID:15128743

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OCA

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-[[Image:1s3n.gif|left|200px]]<br /><applet load="1s3n" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1s3n, resolution 2.50&Aring;" />
 '''Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase'''<br />
 ==Overview==
-Methanococcus jannaschii MJ0936 is a hypothetical protein of unknown, function with over 50 homologs found in many bacteria and Archaea. To help, define the molecular (biochemical and biophysical) function of MJ0936, we, determined its crystal structure at 2.4-A resolution and performed a, series of biochemical screens for catalytic activity. The overall fold of, this single domain protein consists of a four-layered structure formed by, two beta-sheets flanked by alpha-helices on both sides. The crystal, structure suggested its biochemical function to be a nuclease, phosphatase, or nucleotidase, with a requirement for some metal ions., Crystallization in the presence of Ni(2+) or Mn(2+) produced a protein, containing a binuclear metal center in the putative active site formed by, a cluster of conserved residues. Analysis of MJ0936 against a panel of, general enzymatic assays revealed catalytic activity toward, bis-p-nitrophenyl phosphate, an indicator substrate for phosphodiesterases, and nucleases. Significant activity was also found with two other, phosphodiesterase substrates, thymidine 5'-monophosphate p-nitrophenyl, ester and p-nitrophenylphosphorylcholine, but no activity was found for, cAMP or cGMP. Phosphodiesterase activity of MJ0936 had an absolute, requirement for divalent metal ions with Ni(2+) and Mn(2+) being most, effective. Thus, our structural and enzymatic studies have identified the, biochemical function of MJ0936 as that of a novel phosphodiesterase.
+Methanococcus jannaschii MJ0936 is a hypothetical protein of unknown function with over 50 homologs found in many bacteria and Archaea. To help define the molecular (biochemical and biophysical) function of MJ0936, we determined its crystal structure at 2.4-A resolution and performed a series of biochemical screens for catalytic activity. The overall fold of this single domain protein consists of a four-layered structure formed by two beta-sheets flanked by alpha-helices on both sides. The crystal structure suggested its biochemical function to be a nuclease, phosphatase, or nucleotidase, with a requirement for some metal ions. Crystallization in the presence of Ni(2+) or Mn(2+) produced a protein containing a binuclear metal center in the putative active site formed by a cluster of conserved residues. Analysis of MJ0936 against a panel of general enzymatic assays revealed catalytic activity toward bis-p-nitrophenyl phosphate, an indicator substrate for phosphodiesterases and nucleases. Significant activity was also found with two other phosphodiesterase substrates, thymidine 5'-monophosphate p-nitrophenyl ester and p-nitrophenylphosphorylcholine, but no activity was found for cAMP or cGMP. Phosphodiesterase activity of MJ0936 had an absolute requirement for divalent metal ions with Ni(2+) and Mn(2+) being most effective. Thus, our structural and enzymatic studies have identified the biochemical function of MJ0936 as that of a novel phosphodiesterase.
 ==About this Structure==
-S3N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S3N OCA].
+S3N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii] with <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S3N OCA].
 ==Reference==
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 [[Category: Methanocaldococcus jannaschii]]
 [[Category: Single protein]]
-[[Category: BSGC, Berkeley.Structural.Genomics.Center.]]
+[[Category: BSGC, Berkeley Structural Genomics Center.]]
 [[Category: Busso, D.]]
 [[Category: Chen, S.]]
 [[Category: Jancrick, J.]]
 [[Category: Kim, R.]]
-[[Category: Kim, S.H.]]
+[[Category: Kim, S H.]]
 [[Category: Kuznetsova, E.]]
 [[Category: Proudfoot, M.]]
-[[Category: Yakunin, A.F.]]
+[[Category: Yakunin, A F.]]
 [[Category: MN]]
 [[Category: berkeley structural genomics center]]
@@ Line 31: / Line 31: @@
 [[Category: structural genomics]]
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