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New page: left|200px<br /> <applet load="1mh9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mh9, resolution 1.80Å" /> '''Crystal Structure A...
 
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[[Image:1mh9.gif|left|200px]]<br />
<applet load="1mh9" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1mh9, resolution 1.80&Aring;" />
'''Crystal Structure Analysis of deoxyribonucleotidase'''<br />


==Overview==
==Crystal Structure Analysis of deoxyribonucleotidase==
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.
<StructureSection load='1mh9' size='340' side='right'caption='[[1mh9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
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 PO4 and MG 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MH9 OCA].  
</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>
 
<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>
==Reference==
<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>
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]
</table>
[[Category: 5'-nucleotidase]]
== Function ==
[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.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mh/1mh9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bianchi, V.]]
[[Category: Bianchi V]]
[[Category: Nordlund, P.]]
[[Category: Nordlund P]]
[[Category: Rampazzo, C.]]
[[Category: Rampazzo C]]
[[Category: Reichard, P.]]
[[Category: Reichard P]]
[[Category: Rinaldo-Matthis, A.]]
[[Category: Rinaldo-Matthis A]]
[[Category: MG]]
[[Category: PO4]]
[[Category: 4-helix bundle]]
[[Category: rossman fold]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 18:11:11 2007''

Latest revision as of 13:26, 13 March 2024

Crystal Structure Analysis of deoxyribonucleotidase

1mh9, resolution 1.80Å

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