title: Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D.
abstract: 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+).
authors.affiliation: Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
authors.forename: Aswin
authors.initials: A
authors.lastname: Natarajan
authors.forename: Kaushik
authors.initials: K
authors.lastname: Dutta
authors.forename: Deniz B
authors.initials: DB
authors.lastname: Temel
authors.forename: Pravin A
authors.initials: PA
authors.lastname: Nair
authors.forename: Stewart
authors.initials: S
authors.lastname: Shuman
authors.forename: Ranajeet
authors.initials: R
authors.lastname: Ghose
mesh_terms: D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D011088:DNA Ligases / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D005453:Fluorescence; D008670:Metals / Q000737:chemistry; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011550:Pseudomonas aeruginosa / Q000201:enzymology
chemical_list: D004268:DNA-Binding Proteins; D008670:Metals; D004247:DNA; D011088:DNA Ligases
references.citation: Science. 2007 Oct 19;318(5849):456-9
references.pmid: 17947582
references.citation: Chem Rev. 2004 Aug;104(8):3519-40
references.pmid: 15303825
references.citation: J Biomol NMR. 2009 Aug;44(4):213-23
references.pmid: 19548092
references.citation: J Biol Chem. 2010 Feb 12;285(7):4815-25
references.pmid: 20018881
references.citation: J Biol Chem. 2006 May 12;281(19):13412-13423
references.pmid: 16476729
references.citation: J Am Chem Soc. 2009 May 6;131(17):6048-9
references.pmid: 19358609
references.citation: J Biol Chem. 2005 Jan 7;280(1):418-27
references.pmid: 15520014
references.citation: J Biol Chem. 2006 May 19;281(20):13873-81
references.pmid: 16540477
references.citation: Proteins. 2003 Feb 15;50(3):496-506
references.pmid: 12557191
references.citation: J Biol Chem. 2004 May 14;279(20):20594-606
references.pmid: 14985346
references.citation: J Biol Chem. 2005 Jul 15;280(28):25973-81
references.pmid: 15897197
references.citation: J Biol Chem. 2008 Mar 28;283(13):8331-9
references.pmid: 18203718
references.citation: Photochem Photobiol. 1973 Oct;18(4):263-79
references.pmid: 4583619
references.citation: Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1711-6
references.pmid: 16446439
references.citation: Protein Sci. 1996 Feb;5(2):212-20
references.pmid: 8745398
references.citation: J Mol Biol. 2007 Feb 16;366(2):391-405
references.pmid: 17174332
references.citation: Genes Dev. 2008 Feb 15;22(4):512-27
references.pmid: 18281464
references.citation: Methods Mol Biol. 2004;278:379-402
references.pmid: 15318004
references.citation: Mol Cell. 2011 Jan 21;41(2):221-31
references.pmid: 21255731
references.citation: Methods Mol Biol. 2004;278:313-52
references.pmid: 15318002
references.citation: Nat Rev Microbiol. 2007 Nov;5(11):852-61
references.pmid: 17938628
references.citation: Biomol NMR Assign. 2011 Oct;5(2):151-5
references.pmid: 21213076
references.citation: Nucleic Acids Res. 2012 Jan;40(2):828-36
references.pmid: 21965539
references.citation: Biochemistry. 2002 Jan 8;41(1):1-7
references.pmid: 11771996
references.citation: Nucleic Acids Res. 2007;35(11):3631-45
references.pmid: 17488851
references.citation: Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13585-90
references.pmid: 9811843
references.citation: J Biomol NMR. 1996 Dec;8(4):477-86
references.pmid: 9008363
references.citation: Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12822-7
references.pmid: 20616014
references.citation: J Biol Chem. 2005 Oct 7;280(40):33707-15
references.pmid: 16046407
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):221-2
references.pmid: 11125097
references.citation: Nucleic Acids Res. 2011 Apr;39(8):3310-20
references.pmid: 21208981
references.citation: J Biomol NMR. 2011 May;50(1):43-57
references.pmid: 21448735
references.citation: Mol Microbiol. 2011 Jan;79(2):316-30
references.pmid: 21219454