3dzi

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[[Image:3dzi.png|left|200px]]
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==Crystal structure of human CD38 extracellular domain, ribose-5'-phosphate intermediate/GTP complex==
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<StructureSection load='3dzi' size='340' side='right' caption='[[3dzi]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3dzi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DZI FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene>, <scene name='pdbligand=RGT:2-AMINO-9-{5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-RIBOFURANOSYL}-9H-PURIN-6-YL+5-O-PHOSPHONO-BETA-D-RIBOFURANOSIDE'>RGT</scene><br>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dzf|3dzf]], [[3dzg|3dzg]], [[3dzh|3dzh]], [[3dzj|3dzj]], [[3dzk|3dzk]]</td></tr>
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<tr><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 Homo sapiens])</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dzi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dzi RCSB], [http://www.ebi.ac.uk/pdbsum/3dzi PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/3dzi_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Enzymatic utilization of nicotinamide adenine dinucleotide (NAD) has increasingly been shown to have fundamental roles in gene regulation, signal transduction, and protein modification. Many of the processes require the cleavage of the nicotinamide moiety from the substrate and the formation of a reactive intermediate. Using X-ray crystallography, we show that human CD38, an NAD-utilizing enzyme, is capable of catalyzing the cleavage reactions through both covalent and noncovalent intermediates, depending on the substrate used. The covalent intermediate is resistant to further attack by nucleophiles, resulting in mechanism-based enzyme inactivation. The noncovalent intermediate is stabilized mainly through H-bond interactions, but appears to remain reactive. Our structural results favor the proposal of a noncovalent intermediate during normal enzymatic utilization of NAD by human CD38 and provide structural insights into the design of covalent and noncovalent inhibitors targeting NAD-utilization pathways.
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{{STRUCTURE_3dzi| PDB=3dzi | SCENE= }}
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Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38.,Liu Q, Kriksunov IA, Jiang H, Graeff R, Lin H, Lee HC, Hao Q Chem Biol. 2008 Oct 20;15(10):1068-78. PMID:18940667<ref>PMID:18940667</ref>
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===Crystal structure of human CD38 extracellular domain, ribose-5'-phosphate intermediate/GTP complex===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_18940667}}
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==About this Structure==
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[[3dzi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DZI OCA].
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==See Also==
==See Also==
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*[[Cluster of Differentiation 38|Cluster of Differentiation 38]]
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*[[Cluster of Differentiation CD38|Cluster of Differentiation CD38]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:018940667</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Graeff, R.]]
[[Category: Graeff, R.]]

Revision as of 10:51, 29 September 2014

Crystal structure of human CD38 extracellular domain, ribose-5'-phosphate intermediate/GTP complex

3dzi, resolution 1.73Å

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