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4mum

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Revision as of 10:10, 28 December 2022

Crystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase alternative spliced variant

Structural highlights

4mum 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.
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.

Publication Abstract from PubMed

Abstract Human mitochondrial 5'(3')-deoxyribonucleotidase (mdN) catalyzes dephosphorylation of nucleoside monophosphates, and thus helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Mature mdN is a 23-kDa dimeric protein with highest expression levels in the heart, brain and skeletal muscle. We have identified an alternative splice variant of the mdN gene containing an 18-nucleotide insertion encoding 6 amino acids (GKWPAT) at the 3'-end of the penultimate exon 4. We recombinantly expressed this enzyme variant and characterized its biochemical and kinetic properties as well as its three-dimensional structure. Our high-resolution (1.27 A) crystal structure revealed that the insertion forms a loop located in the vicinity of the active site pocket and affects enzyme kinetic parameters as well as protein thermal stability.

Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase.,Pachl P, Fabry M, Veverka V, Brynda J, Rezacova P J Enzyme Inhib Med Chem. 2014 Feb 10. PMID:24506201^[1]

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

References

↑ Pachl P, Fabry M, Veverka V, Brynda J, Rezacova P. Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase. J Enzyme Inhib Med Chem. 2014 Feb 10. PMID:24506201 doi:http://dx.doi.org/10.3109/14756366.2013.879577

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4mum"

Categories: Homo sapiens | Large Structures | Pachl P | Rezacova P

@@ Line 1: / Line 1: @@
 ==Crystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase alternative spliced variant==
-<StructureSection load='4mum' size='340' side='right' caption='[[4mum]], [[Resolution|resolution]] 1.27&Aring;' scene=''>
+<StructureSection load='4mum' size='340' side='right'caption='[[4mum]], [[Resolution|resolution]] 1.27&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4mum]] 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=4MUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MUM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4mum]] 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=4MUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MUM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DNT1, NT5C, UMPH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4mum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mum OCA], [https://pdbe.org/4mum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mum RCSB], [https://www.ebi.ac.uk/pdbsum/4mum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mum ProSAT]</span></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=4mum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mum OCA], [http://pdbe.org/4mum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mum RCSB], [http://www.ebi.ac.uk/pdbsum/4mum PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mum ProSAT]</span></td></tr>
 </table>
+== 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.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Pachl, P]]
+[[Category: Large Structures]]
-[[Category: Rezacova, P]]
+[[Category: Pachl P]]
-[[Category: 5'-nucleotidase]]
+[[Category: Rezacova P]]
-[[Category: Dephosphorylation]]
-[[Category: Had-like]]
-[[Category: Hydrolase]]
-[[Category: Protein conformation]]
-[[Category: Sequence homology]]

4mum

From Proteopedia

Revision as of 10:10, 28 December 2022

Crystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase alternative spliced variant

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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