1z4j

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{{Seed}}
 
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[[Image:1z4j.png|left|200px]]
 
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==Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-monophosphate==
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The line below this paragraph, containing "STRUCTURE_1z4j", creates the "Structure Box" on the page.
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<StructureSection load='1z4j' size='340' side='right'caption='[[1z4j]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1z4j]] 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=1Z4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z4J FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.8&#8491;</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U2P:PHOSPHORIC+ACID+MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL]+ESTER'>U2P</scene></td></tr>
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{{STRUCTURE_1z4j| PDB=1z4j | SCENE= }}
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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=1z4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4j OCA], [https://pdbe.org/1z4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z4j RCSB], [https://www.ebi.ac.uk/pdbsum/1z4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4j ProSAT]</span></td></tr>
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</table>
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== Function ==
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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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== 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/z4/1z4j_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/main_output.php?pdb_ID=1z4j 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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The human mitochondrial deoxyribonucleotidase catalyzes the dephosphorylation of thymidine and deoxyuridine monophosphates and participates in the regulation of the dTTP pool in mitochondria. We present seven structures of the inactive D41N variant of this enzyme in complex with thymidine 3'-monophosphate, thymidine 5'-monophosphate, deoxyuridine 5'-monophosphate, uridine 5'-monophosphate, deoxyguanosine 5'-monophosphate, uridine 2'-monophosphate, and the 5'-monophosphate of the nucleoside analog 3'-deoxy 2'3'-didehydrothymidine, and we draw conclusions about the substrate specificity based on comparisons with enzyme activities. We show that the enzyme's specificity for the deoxyribo form of nucleoside 5'-monophosphates is due to Ile-133, Phe-49, and Phe-102, which surround the 2' position of the sugar and cause an energetically unfavorable environment for the 2'-hydroxyl group of ribonucleoside 5'-monophosphates. The close binding of the 3'-hydroxyl group of nucleoside 5'-monophosphates to the enzyme indicates that nucleoside analog drugs that are substituted with a bulky group at this position will not be good substrates for this enzyme.
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===Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-monophosphate===
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Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase.,Wallden K, Ruzzenente B, Rinaldo-Matthis A, Bianchi V, Nordlund P Structure. 2005 Jul;13(7):1081-8. PMID:16004879<ref>PMID:16004879</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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The line below this paragraph, {{ABSTRACT_PUBMED_16004879}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1z4j" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 16004879 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16004879}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1Z4J is a [[Single protein]] structure of 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=1Z4J OCA].
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==Reference==
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Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase., Wallden K, Ruzzenente B, Rinaldo-Matthis A, Bianchi V, Nordlund P, Structure. 2005 Jul;13(7):1081-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16004879 16004879]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bianchi, V.]]
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[[Category: Bianchi V]]
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[[Category: Nordlund, P.]]
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[[Category: Nordlund P]]
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[[Category: Rinaldo-Matthis, A.]]
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[[Category: Rinaldo-Matthis A]]
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[[Category: Ruzzenente, B.]]
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[[Category: Ruzzenente B]]
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[[Category: Wallden, K.]]
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[[Category: Wallden K]]
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[[Category: Alfa beta fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 16:26:51 2008''
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Current revision

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-monophosphate

PDB ID 1z4j

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