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8 hits found for Nicked DNA

SASDFH6 – ...DNA ligase-A tricomplex in the presence of DNA substrate

Probable exodeoxyribonuclease III protein XthADNA ligase ABeta sliding clampDNA ligase A nicked DNA substrate experimental SAS data
DAMMIF model
Sample: Probable exodeoxyribonuclease III protein XthA monomer, 31 kDa Mycobacterium tuberculosis protein
DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
DNA ligase A nicked DNA substrate dimer, 16 kDa DNA
Buffer: 50 mM Tris pH 8.0, 200 mM NaCl , 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 17
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R
RgGuinier 5.8 nm
Dmax 19.1 nm
VolumePorod 496 nm3

SASDXG9 – ...nicked DNA complex

Aspergillus fumigatus poly(ADP-ribose)polymerase 15'Phosphorylated nicked DNA damage mimetic experimental SAS data
Aspergillus fumigatus poly(ADP-ribose)polymerase 1 5'Phosphorylated nicked DNA damage mimetic Kratky plot
Sample: Aspergillus fumigatus poly(ADP-ribose)polymerase 1 monomer, 74 kDa Aspergillus fumigatus protein
...nicked DNA damage mimetic monomer, 14 kDa DNA
Buffer: 20 mM HEPES, 150 mM NaCl, 2 mM TCEP, 2.5% (v/v) Glycerol, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2024 Nov 14
...DNA binding and catalytic efficiency of fungal PARPs. Nat Commun 17(1) (2026)
Bainbridge AG, Gianga TM, Hussain R, Parkin C, Longhurst AD, Helmstetter N, Farrer RA, Catania S, Siligardi G, Rack JGM
RgGuinier 4.3 nm
Dmax 16.6 nm
VolumePorod 190 nm3

SASDXH9 – ...nicked DNA complex

Aspergillus fumigatus poly(ADP-ribosyl)polymerase 1 dBRCT5'Phosphorylated nicked DNA damage mimetic experimental SAS data
Aspergillus fumigatus poly(ADP-ribosyl)polymerase 1 dBRCT 5'Phosphorylated nicked DNA damage mimetic Kratky plot
Sample: Aspergillus fumigatus poly(ADP-ribosyl)polymerase 1 dBRCT monomer, 58 kDa Aspergillus fumigatus protein
...nicked DNA damage mimetic monomer, 14 kDa DNA
Buffer: 20 mM HEPES, 150 mM NaCl, 2 mM TCEP, 2.5% (v/v) Glycerol, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2024 Nov 14
...DNA binding and catalytic efficiency of fungal PARPs. Nat Commun 17(1) (2026)
Bainbridge AG, Gianga TM, Hussain R, Parkin C, Longhurst AD, Helmstetter N, Farrer RA, Catania S, Siligardi G, Rack JGM
RgGuinier 3.5 nm
Dmax 11.4 nm
VolumePorod 151 nm3

SASDEU5 – ...DNA ligase A

DNA ligase A experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 38 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2018 Sep 27
...DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity Acta Crystallographica Section D Structural Biology 77(6) (2021)
Afsar M, Shukla A, Kumar N, Ramachandran R
RgGuinier 2.4 nm
Dmax 8.8 nm
VolumePorod 69 nm3

SASDEC6 – ...DNA ligase A with NAD+

DNA ligase A experimental SAS data
DAMMIF model
Sample: DNA ligase A monomer, 38 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2018 Oct 6
...DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity Acta Crystallographica Section D Structural Biology 77(6) (2021)
Afsar M, Shukla A, Kumar N, Ramachandran R
RgGuinier 2.4 nm
Dmax 6.2 nm
VolumePorod 94 nm3

SASDG65 – ...DNA ligase A (LigA)

DNA ligase A experimental SAS data
GASBOR model
Sample: DNA ligase A monomer, 37 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 May 21
...DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity Acta Crystallographica Section D Structural Biology 77(6) (2021)
Afsar M, Shukla A, Kumar N, Ramachandran R
RgGuinier 2.7 nm
Dmax 8.9 nm
VolumePorod 68 nm3

SASDDV9 – ...DNA LigaseA with Nicked DNA

DNA ligase ANicked DNA experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Nicked DNA dimer, 16 kDa DNA
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
...DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res (2020)
Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R
RgGuinier 4.4 nm
Dmax 14.8 nm
VolumePorod 262 nm3

SASDEX3 – DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA) in presence of nicked ds DNA

DNA ligase AProbable exodeoxyribonuclease III protein XthANicked DNA experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 33 kDa Mycobacterium tuberculosis protein
Nicked DNA monomer, 8 kDa DNA
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
...DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res (2020)
Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R
RgGuinier 4.5 nm
Dmax 17.1 nm
VolumePorod 117 nm3