1r12: 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:
{{Seed}}
[[Image:1r12.png|left|200px]]


<!--
==Native Aplysia ADP ribosyl cyclase==
The line below this paragraph, containing "STRUCTURE_1r12", creates the "Structure Box" on the page.
<StructureSection load='1r12' size='340' side='right'caption='[[1r12]], [[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'>[[1r12]] is a 2 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=1R12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R12 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r12 OCA], [https://pdbe.org/1r12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r12 RCSB], [https://www.ebi.ac.uk/pdbsum/1r12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r12 ProSAT]</span></td></tr>
{{STRUCTURE_1r12|  PDB=1r12  |  SCENE=  }}
</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/r1/1r12_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=1r12 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.


===Native Aplysia ADP ribosyl cyclase===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1r12" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_15016363}}, adds the Publication Abstract to the page
*[[Cluster of Differentiation CD38|Cluster of Differentiation CD38]]
(as it appears on PubMed at http://www.pubmed.gov), where 15016363 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15016363}}
__TOC__
 
</StructureSection>
==About this Structure==
1R12 is a 2 chains structure of sequences 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=1R12 OCA].
 
==Reference==
<ref group="xtra">PMID:15016363</ref><references group="xtra"/>
[[Category: Aplysia californica]]
[[Category: Aplysia californica]]
[[Category: Graeff, R.]]
[[Category: Large Structures]]
[[Category: Hao, Q.]]
[[Category: Graeff R]]
[[Category: Kriksunov, I A.]]
[[Category: Hao Q]]
[[Category: Lee, H C.]]
[[Category: Kriksunov IA]]
[[Category: Love, M L.]]
[[Category: Lee HC]]
[[Category: Munshi, C.]]
[[Category: Love ML]]
[[Category: Szebenyi, D M.E.]]
[[Category: Munshi C]]
[[Category: Thiel, D J.]]
[[Category: Szebenyi DME]]
[[Category: Adp-ribosyl cyclase]]
[[Category: Thiel DJ]]
[[Category: Ca2+ signalling]]
[[Category: Cyclic adp-ribose]]
[[Category: Naadp]]
[[Category: X-ray crystallography]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:56:22 2009''

Latest revision as of 11:46, 6 November 2024

Native Aplysia ADP ribosyl cyclaseNative Aplysia ADP ribosyl cyclase

Structural highlights

1r12 is a 2 chain structure with sequence from Aplysia californica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

Evolutionary Conservation

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

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.

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[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Chini EN, Chini CC, Kato I, Takasawa S, Okamoto H. CD38 is the major enzyme responsible for synthesis of nicotinic acid-adenine dinucleotide phosphate in mammalian tissues. Biochem J. 2002 Feb 15;362(Pt 1):125-30. PMID:11829748
  2. ↑ Love ML, Szebenyi DM, Kriksunov IA, Thiel DJ, Munshi C, Graeff R, Lee HC, Hao Q. ADP-ribosyl cyclase; crystal structures reveal a covalent intermediate. Structure. 2004 Mar;12(3):477-86. PMID:15016363 doi:http://dx.doi.org/10.1016/j.str.2004.02.006

1r12, 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=1r12&oldid=4200387"