|
|
| (5 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Solution Structure and DNA-binding Properties of the Phosphoesterase Domain of DNA Ligase D== | | ==Solution Structure and DNA-binding Properties of the Phosphoesterase Domain of DNA Ligase D== |
| - | <StructureSection load='2lj6' size='340' side='right' caption='[[2lj6]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''> | + | <StructureSection load='2lj6' size='340' side='right'caption='[[2lj6]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2lj6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ6 OCA]. <br> | + | <table><tr><td colspan='2'>[[2lj6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LJ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LJ6 FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA2138 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2lj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj6 OCA], [https://pdbe.org/2lj6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lj6 RCSB], [https://www.ebi.ac.uk/pdbsum/2lj6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj6 ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lj6 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj6 PDBsum]</span></td></tr> | + | </table> |
| - | <table> | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/LIGD_PSEAE LIGD_PSEAE] With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'-ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide.<ref>PMID:15897197</ref> <ref>PMID:16046407</ref> <ref>PMID:20018881</ref> The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 13: |
Line 15: |
| | Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D.,Natarajan A, Dutta K, Temel DB, Nair PA, Shuman S, Ghose R Nucleic Acids Res. 2012 Mar 1;40(5):2076-88. Epub 2011 Nov 13. PMID:22084199<ref>PMID:22084199</ref> | | Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D.,Natarajan A, Dutta K, Temel DB, Nair PA, Shuman S, Ghose R Nucleic Acids Res. 2012 Mar 1;40(5):2076-88. Epub 2011 Nov 13. PMID:22084199<ref>PMID:22084199</ref> |
| | | | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2lj6" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Pseudomonas aeruginosa]] | | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Dutta, K.]] | + | [[Category: Dutta K]] |
| - | [[Category: Ghose, R.]] | + | [[Category: Ghose R]] |
| - | [[Category: Natarajan, A.]] | + | [[Category: Natarajan A]] |
| - | [[Category: Shuman, S.]] | + | [[Category: Shuman S]] |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Phosphoesterase]]
| + | |
| Structural highlights
Function
LIGD_PSEAE With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'-ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide.[1] [2] [3] The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting.
Publication Abstract from PubMed
The phosphoesterase (PE) domain of the bacterial DNA repair enzyme LigD possesses distinctive manganese-dependent 3'-phosphomonoesterase and 3'-phosphodiesterase activities. PE exemplifies a new family of DNA end-healing enzymes found in all phylogenetic domains. Here, we determined the structure of the PE domain of Pseudomonas aeruginosa LigD (PaePE) using solution NMR methodology. PaePE has a disordered N-terminus and a well-folded core that differs in instructive ways from the crystal structure of a PaePE*Mn(2+)* sulfate complex, especially at the active site that is found to be conformationally dynamic. Chemical shift perturbations in the presence of primer-template duplexes with 3'-deoxynucleotide, 3'-deoxynucleotide 3'-phosphate, or 3' ribonucleotide termini reveal the surface used by PaePE to bind substrate DNA and suggest a more efficient engagement in the presence of a 3'-ribonucleotide. Spectral perturbations measured in the presence of weakly catalytic (Cd(2+)) and inhibitory (Zn(2+)) metals provide evidence for significant conformational changes at and near the active site, compared to the relatively modest changes elicited by Mn(2+).
Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D.,Natarajan A, Dutta K, Temel DB, Nair PA, Shuman S, Ghose R Nucleic Acids Res. 2012 Mar 1;40(5):2076-88. Epub 2011 Nov 13. PMID:22084199[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhu H, Shuman S. Novel 3'-ribonuclease and 3'-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D. J Biol Chem. 2005 Jul 15;280(28):25973-81. PMID:15897197 doi:10.1074/jbc.M504002200
- ↑ Zhu H, Wang LK, Shuman S. Essential constituents of the 3'-phosphoesterase domain of bacterial DNA ligase D, a nonhomologous end-joining enzyme. J Biol Chem. 2005 Oct 7;280(40):33707-15. PMID:16046407 doi:10.1074/jbc.M506838200
- ↑ Zhu H, Shuman S. Gap filling activities of Pseudomonas DNA ligase D (LigD) polymerase and functional interactions of LigD with the DNA end-binding Ku protein. J Biol Chem. 2010 Feb 12;285(7):4815-25. PMID:20018881 doi:10.1074/jbc.M109.073874
- ↑ Natarajan A, Dutta K, Temel DB, Nair PA, Shuman S, Ghose R. Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D. Nucleic Acids Res. 2012 Mar 1;40(5):2076-88. Epub 2011 Nov 13. PMID:22084199 doi:10.1093/nar/gkr950
|
