1vcd: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1vcd.png|left|200px]]


<!--
==Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1==
The line below this paragraph, containing "STRUCTURE_1vcd", creates the "Structure Box" on the page.
<StructureSection load='1vcd' size='340' side='right'caption='[[1vcd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1vcd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VCD FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_1vcd| PDB=1vcd |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcd OCA], [https://pdbe.org/1vcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vcd RCSB], [https://www.ebi.ac.uk/pdbsum/1vcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcd ProSAT], [https://www.topsan.org/Proteins/RSGI/1vcd TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NDX1_THETH 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.<ref>PMID:15024014</ref>
== 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/vc/1vcd_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/main_output.php?pdb_ID=1vcd ConSurf].
<div style="clear:both"></div>


===Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1===
==See Also==
 
*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1VCD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCD OCA].
__TOC__
[[Category: Thermus thermophilus]]
</StructureSection>
[[Category: Iwai, T.]]
[[Category: Large Structures]]
[[Category: Kuramitsu, S.]]
[[Category: Thermus thermophilus HB8]]
[[Category: Masui, R.]]
[[Category: Iwai T]]
[[Category: Nakagawa, N.]]
[[Category: Kuramitsu S]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Masui R]]
[[Category: Ap6a]]
[[Category: Nakagawa N]]
[[Category: Diadenosine polyphosphate]]
[[Category: Hydrolase]]
[[Category: Nudix protein]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Thermus thermophilus hb8]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 15:53:10 2008''

Latest revision as of 03:01, 28 December 2023

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 Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:,
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.

See Also

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

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=1vcd&oldid=4007446"