1r15: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1r15.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1r15", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1r15|  PDB=1r15  |  SCENE=  }}
'''Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P'''


==Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P==
<StructureSection load='1r15' size='340' side='right'caption='[[1r15]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1r15]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aplysia_californica Aplysia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R15 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene>, <scene name='pdbligand=NCA:NICOTINAMIDE'>NCA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r15 OCA], [https://pdbe.org/1r15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r15 RCSB], [https://www.ebi.ac.uk/pdbsum/1r15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r15 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NADA_APLCA NADA_APLCA] Synthesizes the second messagers cyclic ADP-ribose and nicotinate-adenine dinucleotide phosphate, the former a second messenger for calcium mobilization from endoplasmic reticulum. Also has cADPr hydrolase activity.<ref>PMID:11829748</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/r1/1r15_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1r15 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
ADP-ribosyl cyclase catalyzes the elimination of nicotinamide from NAD and cyclization to cADPR, a known second messenger in cellular calcium signaling pathways. We have determined to 2.0 A resolution the structure of Aplysia cyclase with ribose-5-phosphate bound covalently at C3' and with the base exchange substrate (BES), pyridylcarbinol, bound to the active site. In addition, further refinement at 2.4 A resolution of the structure of nicotinamide-bound cyclase, which was previously reported, reveals that ribose-5-phosphate is also covalently bound in this structure, and a second nicotinamide site was identified. The structures of native and mutant Glu179Ala cyclase were also solved to 1.7 and 2.0 A respectively. It is proposed that the second nicotinamide site serves to promote cyclization by clearing the active site of the nicotinamide byproduct. Moreover, a ribosylation mechanism can be proposed in which the cyclization reaction proceeds through a covalently bound intermediate.


==Overview==
ADP-ribosyl cyclase; crystal structures reveal a covalent intermediate.,Love ML, Szebenyi DM, Kriksunov IA, Thiel DJ, Munshi C, Graeff R, Lee HC, Hao Q Structure. 2004 Mar;12(3):477-86. PMID:15016363<ref>PMID:15016363</ref>
ADP-ribosyl cyclase catalyzes the elimination of nicotinamide from NAD and cyclization to cADPR, a known second messenger in cellular calcium signaling pathways. We have determined to 2.0 A resolution the structure of Aplysia cyclase with ribose-5-phosphate bound covalently at C3' and with the base exchange substrate (BES), pyridylcarbinol, bound to the active site. In addition, further refinement at 2.4 A resolution of the structure of nicotinamide-bound cyclase, which was previously reported, reveals that ribose-5-phosphate is also covalently bound in this structure, and a second nicotinamide site was identified. The structures of native and mutant Glu179Ala cyclase were also solved to 1.7 and 2.0 A respectively. It is proposed that the second nicotinamide site serves to promote cyclization by clearing the active site of the nicotinamide byproduct. Moreover, a ribosylation mechanism can be proposed in which the cyclization reaction proceeds through a covalently bound intermediate.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1R15 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aplysia_californica Aplysia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R15 OCA].
</div>
<div class="pdbe-citations 1r15" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
ADP-ribosyl cyclase; crystal structures reveal a covalent intermediate., Love ML, Szebenyi DM, Kriksunov IA, Thiel DJ, Munshi C, Graeff R, Lee HC, Hao Q, Structure. 2004 Mar;12(3):477-86. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15016363 15016363]
*[[Cluster of Differentiation CD38|Cluster of Differentiation CD38]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aplysia californica]]
[[Category: Aplysia californica]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Graeff, R.]]
[[Category: Graeff R]]
[[Category: Hao, Q.]]
[[Category: Hao Q]]
[[Category: Kriksunov, I A.]]
[[Category: Kriksunov IA]]
[[Category: Lee, H C.]]
[[Category: Lee HC]]
[[Category: Love, M L.]]
[[Category: Love ML]]
[[Category: Munshi, C.]]
[[Category: Munshi C]]
[[Category: Szebenyi, D M.E.]]
[[Category: Szebenyi DME]]
[[Category: Thiel, D J.]]
[[Category: Thiel DJ]]
[[Category: Adp-ribosyl cyclase]]
[[Category: Ca2+ signalling]]
[[Category: Cyclic adp-ribose]]
[[Category: Naadp]]
[[Category: X-ray crystallography]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 06:56:57 2008''
Retrieved from "https://proteopedia.org/1r15"