1mh9

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[[Image:1mh9.jpg|left|200px]]<br /><applet load="1mh9" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1mh9, resolution 1.80&Aring;" />
 
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'''Crystal Structure Analysis of deoxyribonucleotidase'''<br />
 
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==Overview==
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==Crystal Structure Analysis of deoxyribonucleotidase==
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5' nucleotidases are ubiquitous enzymes that dephosphorylate nucleoside monophosphates and participate in the regulation of nucleotide pools. The mitochondrial 5'-(3') deoxyribonucleotidase (dNT-2) specifically dephosphorylates dUMP and dTMP, thereby protecting mitochondrial DNA replication from excess dTTP. We have solved the structure of dNT-2, the first of a mammalian 5' nucleotidase. The structure reveals a relationship to the HAD family, members of which use an aspartyl nucleophile as their common catalytic strategy, with a phosphoserine phosphatase as the most similar neighbor. A structure-based sequence alignment of dNT-2 with other 5' nucleotidases also suggests a common origin for these enzymes. Here we study the structures of dNT-2 in complex with bound phosphate and beryllium trifluoride plus thymidine as model for a phosphoenzyme-product complex. Based on these structures, determinants for substrate specificity recognition and the catalytic action of dNT-2 are outlined.
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<StructureSection load='1mh9' size='340' side='right'caption='[[1mh9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1mh9]] 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=1MH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MH9 FirstGlance]. <br>
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1MH9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MH9 OCA].
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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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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==Reference==
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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=1mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mh9 OCA], [https://pdbe.org/1mh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mh9 RCSB], [https://www.ebi.ac.uk/pdbsum/1mh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mh9 ProSAT]</span></td></tr>
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Crystal structure of a human mitochondrial deoxyribonucleotidase., Rinaldo-Matthis A, Rampazzo C, Reichard P, Bianchi V, Nordlund P, Nat Struct Biol. 2002 Oct;9(10):779-87. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12352955 12352955]
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</table>
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[[Category: 5'-nucleotidase]]
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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/mh/1mh9_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=1mh9 ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[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: Rampazzo, C.]]
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[[Category: Rampazzo C]]
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[[Category: Reichard, P.]]
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[[Category: Reichard P]]
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[[Category: Rinaldo-Matthis, A.]]
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[[Category: Rinaldo-Matthis A]]
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[[Category: MG]]
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[[Category: PO4]]
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[[Category: 4-helix bundle]]
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[[Category: rossman fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:55:10 2008''
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Current revision

Crystal Structure Analysis of deoxyribonucleotidase

PDB ID 1mh9

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