1dek: Difference between revisions

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<StructureSection load='1dek' size='340' side='right'caption='[[1dek]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1dek' size='340' side='right'caption='[[1dek]], [[Resolution|resolution]] 2.00&Aring;' 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://proteopedia.org/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" id="ligandDat"><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='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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/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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</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=1dek ConSurf].
</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=1dek ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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<ref>PMID:8670851</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dek" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bpt4]]
[[Category: Escherichia virus T4]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Sebastiao, P]]
[[Category: Sebastiao P]]
[[Category: Teplyakov, A]]
[[Category: Teplyakov A]]
[[Category: Phosphotransferase]]
[[Category: Transferase]]

Revision as of 12:49, 20 March 2024

DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMPDEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP

Structural highlights

1dek is a 2 chain structure with sequence from Escherichia virus T4. 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

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.

References

  1. ↑ 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

1dek, resolution 2.00Å

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