2h6e: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2h6e.gif|left|200px]]


{{Structure
==Crystal structure of the D-arabinose dehydrogenase from Sulfolobus solfataricus==
|PDB= 2h6e |SIZE=350|CAPTION= <scene name='initialview01'>2h6e</scene>, resolution 1.80&Aring;
<StructureSection load='2h6e' size='340' side='right'caption='[[2h6e]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
<table><tr><td colspan='2'>[[2h6e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H6E FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/D-arabinose_1-dehydrogenase_(NAD(P)(+)) D-arabinose 1-dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.117 1.1.1.117] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
|GENE= Adh-4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2h6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h6e OCA], [https://pdbe.org/2h6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h6e RCSB], [https://www.ebi.ac.uk/pdbsum/2h6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h6e ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2h6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h6e OCA], [http://www.ebi.ac.uk/pdbsum/2h6e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2h6e RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/Q97YM2_SACS2 Q97YM2_SACS2]
 
== Evolutionary Conservation ==
'''Crystal structure of the D-arabinose dehydrogenase from Sulfolobus solfataricus'''
[[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/h6/2h6e_consurf.spt"</scriptWhenChecked>
Sulfolobus solfataricus metabolizes the five-carbon sugar d-arabinose to 2-oxoglutarate by an inducible pathway consisting of dehydrogenases and dehydratases. Here we report the crystal structure and biochemical properties of the first enzyme of this pathway: the d-arabinose dehydrogenase. The AraDH structure was solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure revealed a catalytic and cofactor binding domain, typically present in mesophilic and thermophilic alcohol dehydrogenases. Cofactor modeling showed the presence of a phosphate binding pocket sequence motif (SRS-X2-H), which is likely to be responsible for the enzyme's preference for NADP+. The homo-tetrameric enzyme is specific for d-arabinose, l-fucose, l-galactose and d-ribose, which could be explained by the hydrogen bonding patterns of the C3 and C4 hydroxyl groups observed in substrate docking simulations. The enzyme optimally converts sugars at pH 8.2 and 91 degrees C, and displays a half-life of 42 and 26 min at 85 and 90 degrees C, respectively, indicating that the enzyme is thermostable at physiological operating temperatures of 80 degrees C. The structure represents the first crystal structure of an NADP+-dependent member of the medium-chain dehydrogenase/reductase (MDR) superfamily from Archaea.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
2H6E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H6E 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=2h6e ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus., Brouns SJ, Turnbull AP, Willemen HL, Akerboom J, van der Oost J, J Mol Biol. 2007 Aug 31;371(5):1249-60. Epub 2007 Jun 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17610898 17610898]
</StructureSection>
[[Category: D-arabinose 1-dehydrogenase (NAD(P)(+))]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Saccharolobus solfataricus P2]]
[[Category: Sulfolobus solfataricus]]
[[Category: Akerboom J]]
[[Category: Akerboom, J.]]
[[Category: Brouns SJJ]]
[[Category: Brouns, S J.J.]]
[[Category: De Vos WM]]
[[Category: Oost, J Van der.]]
[[Category: Turnbull AP]]
[[Category: Turnbull, A P.]]
[[Category: Van der Oost J]]
[[Category: Vos, W M.De.]]
[[Category: Willemen HLDM]]
[[Category: Willemen, H L.D M]]
[[Category: medium chain alcohol dehydrogenase]]
[[Category: rossman fold]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:26:05 2008''
Retrieved from "https://proteopedia.org/2h6e"