1dek: Difference between revisions
New page: left|200px<br /><applet load="1dek" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dek, resolution 2.0Å" /> '''DEOXYNUCLEOSIDE MONOP... |
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[[Image:1dek.jpg|left|200px]]<br /><applet load="1dek" size=" | [[Image:1dek.jpg|left|200px]]<br /><applet load="1dek" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1dek, resolution 2.0Å" /> | caption="1dek, resolution 2.0Å" /> | ||
'''DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP'''<br /> | '''DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP'''<br /> | ||
==Overview== | ==Overview== | ||
NMP kinases catalyse the phosphorylation of the canonical nucleotides to | 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. | ||
==About this Structure== | ==About this Structure== | ||
1DEK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with MG and DGP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http:// | 1DEK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=DGP:'>DGP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DEK OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:53 2008'' | ||
Revision as of 13:15, 21 February 2008
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DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP
OverviewOverview
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.
About this StructureAbout this Structure
1DEK is a Single protein structure of sequence from Bacteriophage t4 with and as ligands. Active as (Deoxy)nucleoside-phosphate kinase, with EC number 2.7.4.13 Full crystallographic information is available from OCA.
ReferenceReference
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
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