1vcd: Difference between revisions

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==Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1==
==Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1==
<StructureSection load='1vcd' size='340' side='right' caption='[[1vcd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='1vcd' size='340' side='right' caption='[[1vcd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vc8|1vc8]], [[1vc9|1vc9]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vc8|1vc8]], [[1vc9|1vc9]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndx1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndx1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcd OCA], [http://pdbe.org/1vcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vcd RCSB], [http://www.ebi.ac.uk/pdbsum/1vcd PDBsum], [http://www.topsan.org/Proteins/RSGI/1vcd TOPSAN]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcd OCA], [http://pdbe.org/1vcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vcd RCSB], [http://www.ebi.ac.uk/pdbsum/1vcd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcd ProSAT], [http://www.topsan.org/Proteins/RSGI/1vcd TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/1vcd_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/1vcd_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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].
</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=1vcd ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
== References ==
== References ==

Revision as of 10:13, 4 April 2018

Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1

Structural highlights

1vcd is a 2 chain structure with sequence from Thet8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Gene:ndx1 (THET8)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[NDX1_THETH] Specifically hydrolyzes (di)adenosine polyphosphates but not ATP or diadenosine triphosphate, generating ATP as the product. Diadenosine hexaphosphate (Ap6A) is the preferred substrate and its hydrolyzation yields 2 ATP. It is the only enzyme that symmetrically hydrolyzes Ap6A. It also hydrolyzes diadenosine pentaphosphate (Ap5A), diadenosine tetraphosphate (Ap4A), adenosine tetraphosphate (p4A) to produce ATP and ADP, ATP and AMP, ATP and inorganic orthophosphate, respectively.[1]

Evolutionary Conservation

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

References

  1. ↑ Iwai T, Kuramitsu S, Masui R. The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine hexaphosphate hydrolase with a novel activity. J Biol Chem. 2004 May 21;279(21):21732-9. Epub 2004 Mar 15. PMID:15024014 doi:http://dx.doi.org/10.1074/jbc.M312018200

1vcd, resolution 1.70Å

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