1s3n: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1s3n.gif|left|200px]]


{{Structure
==Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase==
|PDB= 1s3n |SIZE=350|CAPTION= <scene name='initialview01'>1s3n</scene>, resolution 2.50&Aring;
<StructureSection load='1s3n' size='340' side='right'caption='[[1s3n]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>
<table><tr><td colspan='2'>[[1s3n]] is a 2 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=1S3N FirstGlance]. <br>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0622 COG0622]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s3n OCA], [https://pdbe.org/1s3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s3n RCSB], [https://www.ebi.ac.uk/pdbsum/1s3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s3n ProSAT], [https://www.topsan.org/Proteins/BSGC/1s3n TOPSAN]</span></td></tr>
|RELATEDENTRY=[[1s3m|1S3M]]
</table>
|RESOURCES=<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.ebi.ac.uk/pdbsum/1s3n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1s3n RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/P936_METJA P936_METJA] Shows phosphodiesterase activity, hydrolyzing phosphodiesters bonds in the artificial chromogenic substrates bis-p-nitrophenyl phosphate (bis-pNPP), and less efficiently thymidine 5'-monophosphate p-nitrophenyl ester (pNP-TMP) and p-nitrophenylphosphorylcholine (pNPPC). No catalytic activity was found toward cAMP or cGMP, nucleotides or phospholipase substrates such as phosphatidylcholine. The physiological substrate is unknown.
 
== Evolutionary Conservation ==
'''Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s3/1s3n_consurf.spt"</scriptWhenChecked>
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.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
1S3N is a [[Single protein]] structure of 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].  
</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/main_output.php?pdb_ID=1s3n ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
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:[http://www.ncbi.nlm.nih.gov/pubmed/15128743 15128743]
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Single protein]]
[[Category: Busso D]]
[[Category: BSGC, Berkeley Structural Genomics Center.]]
[[Category: Chen S]]
[[Category: Busso, D.]]
[[Category: Jancrick J]]
[[Category: Chen, S.]]
[[Category: Kim R]]
[[Category: Jancrick, J.]]
[[Category: Kim S-H]]
[[Category: Kim, R.]]
[[Category: Kuznetsova E]]
[[Category: Kim, S H.]]
[[Category: Proudfoot M]]
[[Category: Kuznetsova, E.]]
[[Category: Yakunin AF]]
[[Category: Proudfoot, M.]]
[[Category: Yakunin, A F.]]
[[Category: berkeley structural genomics center]]
[[Category: bsgc structure funded by nih]]
[[Category: di-metal-binding]]
[[Category: phosphodiesterase/nuclease]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:36:53 2008''

Latest revision as of 11:28, 14 February 2024

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.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

P936_METJA Shows phosphodiesterase activity, hydrolyzing phosphodiesters bonds in the artificial chromogenic substrates bis-p-nitrophenyl phosphate (bis-pNPP), and less efficiently thymidine 5'-monophosphate p-nitrophenyl ester (pNP-TMP) and p-nitrophenylphosphorylcholine (pNPPC). No catalytic activity was found toward cAMP or cGMP, nucleotides or phospholipase substrates such as phosphatidylcholine. The physiological substrate is unknown.

Evolutionary Conservation

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

1s3n, resolution 2.50Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1s3n&oldid=4054740"