1s3n: Difference between revisions

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[[Image:1s3n.png|left|200px]]
==Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase==
<StructureSection load='1s3n' size='340' side='right' caption='[[1s3n]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1s3n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S3N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S3N FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1s3m|1s3m]]</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1s3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s3n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s3n RCSB], [http://www.ebi.ac.uk/pdbsum/1s3n PDBsum], [http://www.topsan.org/Proteins/BSGC/1s3n TOPSAN]</span></td></tr>
<table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s3/1s3n_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


{{STRUCTURE_1s3n|  PDB=1s3n  |  SCENE=  }}
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<ref>PMID:15128743</ref>


===Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_15128743}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[1s3n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S3N OCA].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:015128743</ref><references group="xtra"/>
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: BSGC, Berkeley Structural Genomics Center.]]
[[Category: BSGC, Berkeley Structural Genomics Center.]]

Revision as of 16:54, 29 September 2014

Structural and Functional Characterization of a Novel Archaeal PhosphodiesteraseStructural and Functional Characterization of a Novel Archaeal Phosphodiesterase

Structural highlights

1s3n is a 2 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:1s3m
Resources:FirstGlance, OCA, RCSB, PDBsum, TOPSAN

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Chen S, Yakunin AF, Kuznetsova E, Busso D, Pufan R, Proudfoot M, Kim R, Kim SH. Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii. J Biol Chem. 2004 Jul 23;279(30):31854-62. Epub 2004 May 5. PMID:15128743 doi:http://dx.doi.org/10.1074/jbc.M401059200

1s3n, resolution 2.50Å

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