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| | ==DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP== | | ==DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP== |
| - | <StructureSection load='1dek' size='340' side='right' caption='[[1dek]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='1dek' size='340' side='right'caption='[[1dek]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1dek]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DEK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1dek]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DEK 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]] 2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></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>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=1dek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dek OCA], [https://pdbe.org/1dek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dek RCSB], [https://www.ebi.ac.uk/pdbsum/1dek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dek ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(Deoxy)nucleoside-phosphate_kinase (Deoxy)nucleoside-phosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.13 2.7.4.13] </span></td></tr>
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| - | <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=1dek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dek OCA], [http://pdbe.org/1dek PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dek RCSB], [http://www.ebi.ac.uk/pdbsum/1dek PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dek ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DNMK_BPT4 DNMK_BPT4]] Phosphorylates dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The phosphorylation of 5-hydroxymethyl-dCMP represents the first step in the replacement of cytosine by hydroxymethylcytosine in new viral DNA genomes.<ref>PMID:5338507</ref> | + | [https://www.uniprot.org/uniprot/DNMK_BPT4 DNMK_BPT4] Phosphorylates dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The phosphorylation of 5-hydroxymethyl-dCMP represents the first step in the replacement of cytosine by hydroxymethylcytosine in new viral DNA genomes.<ref>PMID:5338507</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpt4]] | + | [[Category: Escherichia virus T4]] |
| - | [[Category: Sebastiao, P]] | + | [[Category: Large Structures]] |
| - | [[Category: Teplyakov, A]] | + | [[Category: Sebastiao P]] |
| - | [[Category: Phosphotransferase]] | + | [[Category: Teplyakov A]] |
| - | [[Category: Transferase]]
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| Structural highlights
Function
DNMK_BPT4 Phosphorylates dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The phosphorylation of 5-hydroxymethyl-dCMP represents the first step in the replacement of cytosine by hydroxymethylcytosine in new viral DNA genomes.[1]
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
NMP kinases catalyse the phosphorylation of the canonical nucleotides to the corresponding diphosphates using ATP as a phosphate donor. Bacteriophage T4 deoxynucleotide kinase (DNK) is the only member of this family of enzymes that recognizes three structurally dissimilar nucleotides: dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The crystal structure of DNK with its substrate dGMP has been determined at 2.0 A resolution by single isomorphous replacement. The structure of the ternary complex with dGMP and ATP has been determined at 2.2 A resolution. The polypeptide chain of DNK is folded into two domains of equal size, one of which resembles the mononucleotide binding motif with the glycine-rich P-loop. The second domain, consisting of five alpha-helices, forms the NMP binding pocket. A hinge connection between the domains allows for large movements upon substrate binding which are not restricted by dimerization of the enzyme. The mechanism of active centre formation via domain closure is described. Comparison with other P-loop-containing proteins indicates an induced-fit mode of NTP binding. Protein-substrate interactions observed at the NMP and NTP sites provide the basis for understanding the principles of nucleotide discrimination.
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.,Teplyakov A, Sebastiao P, Obmolova G, Perrakis A, Brush GS, Bessman MJ, Wilson KS EMBO J. 1996 Jul 15;15(14):3487-97. PMID:8670851[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Duckworth DH, Bessman MJ. The enzymology of virus-infected bacteria. X. A biochemical-genetic study of the deoxynucleotide kinase induced by wild type and amber mutants of phage T4. J Biol Chem. 1967 Jun 25;242(12):2877-85. PMID:5338507
- ↑ Teplyakov A, Sebastiao P, Obmolova G, Perrakis A, Brush GS, Bessman MJ, Wilson KS. Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP. EMBO J. 1996 Jul 15;15(14):3487-97. PMID:8670851
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