6edr: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 6edr is ~~ON HOLD until Paper~~ Publication

==Crystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+==

== Structural highlights ==

<table><tr><td colspan='2'>[[6edr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EDR FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZNA:[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>ZNA</scene></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CD38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6edr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edr OCA], [http://pdbe.org/6edr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6edr RCSB], [http://www.ebi.ac.uk/pdbsum/6edr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6edr ProSAT]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN]] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.

== Publication Abstract from PubMed ==

Nicotinamide adenine dinucleotide (NAD(+)) is an essential cofactor participating in a variety of important enzyme-catalyzed physiological and pathophysiological processes. Analogues of NAD(+) provide key and valuable agents for investigating NAD(+)-dependent enzymes. In this study, we report the preparation of a novel stable NAD(+) mimic, 4'-thioribose NAD(+) (S-NAD(+)), using a facile and efficient chemoenzymatic approach. Substrate activity assays indicated the resulting S-NAD(+) is chemically inert to human CD38 and sirtuin 2 enzymes, but capable of participating in redox reactions in a manner similar to NAD(+). X-ray crystallographic analysis revealed binding of S-NAD(+) to the active site of human CD38 and critical residues involved in leaving group activation and catalysis. By more closely mimicking NAD(+) in geometry and electrostatics, the generated S-NAD(+) offers a unique and important tool that can be extended to study enzymes utilizing NAD(+).

~~Authors~~:

Facile chemoenzymatic synthesis of a novel stable mimic of NAD().,Dai Z, Zhang XN, Nasertorabi F, Cheng Q, Pei H, Louie SG, Stevens RC, Zhang Y Chem Sci. 2018 Oct 15;9(44):8337-8342. doi: 10.1039/c8sc03899f. eCollection 2018 , Nov 28. PMID:30568770<ref>PMID:30568770</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Human]]

[[Category: Large Structures]]

[[Category: Cheng, Q]]

[[Category: Dai, Z]]

[[Category: Louie, S G]]

[[Category: Nasertorabi, F]]

[[Category: Pei, H]]

[[Category: Stevens, C R]]

[[Category: Zhang, X N]]

[[Category: Zhang, Y]]

[[Category: Cd38]]

[[Category: Hydrolase]]

[[Category: Hydrolase-hydrolase inhibitor complex]]

[[Category: Inhibitor]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6edr is ON HOLD  until Paper Publication
+==Crystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+==
+<StructureSection load='6edr' size='340' side='right'caption='[[6edr]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6edr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EDR FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZNA:[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>ZNA</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CD38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6edr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edr OCA], [http://pdbe.org/6edr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6edr RCSB], [http://www.ebi.ac.uk/pdbsum/6edr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6edr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN]] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nicotinamide adenine dinucleotide (NAD(+)) is an essential cofactor participating in a variety of important enzyme-catalyzed physiological and pathophysiological processes. Analogues of NAD(+) provide key and valuable agents for investigating NAD(+)-dependent enzymes. In this study, we report the preparation of a novel stable NAD(+) mimic, 4'-thioribose NAD(+) (S-NAD(+)), using a facile and efficient chemoenzymatic approach. Substrate activity assays indicated the resulting S-NAD(+) is chemically inert to human CD38 and sirtuin 2 enzymes, but capable of participating in redox reactions in a manner similar to NAD(+). X-ray crystallographic analysis revealed binding of S-NAD(+) to the active site of human CD38 and critical residues involved in leaving group activation and catalysis. By more closely mimicking NAD(+) in geometry and electrostatics, the generated S-NAD(+) offers a unique and important tool that can be extended to study enzymes utilizing NAD(+).
-Authors:
+Facile chemoenzymatic synthesis of a novel stable mimic of NAD().,Dai Z, Zhang XN, Nasertorabi F, Cheng Q, Pei H, Louie SG, Stevens RC, Zhang Y Chem Sci. 2018 Oct 15;9(44):8337-8342. doi: 10.1039/c8sc03899f. eCollection 2018 , Nov 28. PMID:30568770<ref>PMID:30568770</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6edr" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
+[[Category: Cheng, Q]]
+[[Category: Dai, Z]]
+[[Category: Louie, S G]]
+[[Category: Nasertorabi, F]]
+[[Category: Pei, H]]
+[[Category: Stevens, C R]]
+[[Category: Zhang, X N]]
+[[Category: Zhang, Y]]
+[[Category: Cd38]]
+[[Category: Hydrolase]]
+[[Category: Hydrolase-hydrolase inhibitor complex]]
+[[Category: Inhibitor]]