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1z4p

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Current revision

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyriboguanosine 5'-monophosphate

Structural highlights

1z4p is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wallden K, Ruzzenente B, Rinaldo-Matthis A, Bianchi V, Nordlund P. Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase. Structure. 2005 Jul;13(7):1081-8. PMID:16004879 doi:http://dx.doi.org/10.1016/j.str.2005.04.023

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1z4p"

@@ Line 3: / Line 3: @@
 <StructureSection load='1z4p' size='340' side='right'caption='[[1z4p]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1z4p]] 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=1Z4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1z4p]] 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=1Z4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z4P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1z4i|1z4i]], [[1z4j|1z4j]], [[1z4k|1z4k]], [[1z4l|1z4l]], [[1z4m|1z4m]], [[1z4q|1z4q]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<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=1z4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4p OCA], [http://pdbe.org/1z4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z4p RCSB], [http://www.ebi.ac.uk/pdbsum/1z4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4p ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4p OCA], [https://pdbe.org/1z4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z4p RCSB], [https://www.ebi.ac.uk/pdbsum/1z4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4p ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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.
+[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]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Bianchi, V]]
+[[Category: Bianchi V]]
-[[Category: Nordlund, P]]
+[[Category: Nordlund P]]
-[[Category: Rinaldo-Matthis, A]]
+[[Category: Rinaldo-Matthis A]]
-[[Category: Ruzzenente, B]]
+[[Category: Ruzzenente B]]
-[[Category: Wallden, K]]
+[[Category: Wallden K]]
-[[Category: Alfa beta fold]]
-[[Category: Hydrolase]]

1z4p

From Proteopedia

Current revision

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyriboguanosine 5'-monophosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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