4l6a

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==Structure of human mitochondrial 5'(3')-deoxyribonucleotidase==
==Structure of human mitochondrial 5'(3')-deoxyribonucleotidase==
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<StructureSection load='4l6a' size='340' side='right' caption='[[4l6a]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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<StructureSection load='4l6a' size='340' side='right'caption='[[4l6a]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4l6a]] is a 1 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=4L6A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L6A FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4l6a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L6A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L6A FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4l6c|4l6c]]</td></tr>
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<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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DNT2, NT5M ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4l6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l6a OCA], [https://pdbe.org/4l6a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l6a RCSB], [https://www.ebi.ac.uk/pdbsum/4l6a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l6a ProSAT]</span></td></tr>
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<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=4l6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l6a OCA], [http://pdbe.org/4l6a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l6a RCSB], [http://www.ebi.ac.uk/pdbsum/4l6a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l6a ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/NT5M_HUMAN NT5M_HUMAN]] Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
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[https://www.uniprot.org/uniprot/NT5M_HUMAN NT5M_HUMAN] Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 A) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 A) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.
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Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.,Pachl P, Fabry M, Rosenberg I, Simak O, Rezacova P, Brynda J Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):461-70. doi:, 10.1107/S1399004713030502. Epub 2014 Jan 29. PMID:24531480<ref>PMID:24531480</ref>
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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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<div class="pdbe-citations 4l6a" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Human]]
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[[Category: Homo sapiens]]
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[[Category: Brynda, J]]
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[[Category: Large Structures]]
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[[Category: Pachl, P]]
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[[Category: Brynda J]]
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[[Category: Rezacova, P]]
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[[Category: Pachl P]]
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[[Category: Dephosphorylation]]
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[[Category: Rezacova P]]
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[[Category: Had-like]]
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[[Category: Hydrolase]]
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[[Category: Phosphorylation]]
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[[Category: Protein conformation]]
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[[Category: Sequence homology]]
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Current revision

Structure of human mitochondrial 5'(3')-deoxyribonucleotidase

PDB ID 4l6a

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