Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex

Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R
International Journal of Biological Macromolecules (2022 Nov)

doi: 10.1016/j.ijbiomac.2022.11.094 		Submitted to SASBDB: 2019 May 24
Published in SASBDB:

SASDFE6 – Sliding beta clamp

Beta sliding clamp experimental SAS data
GASBOR model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
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 15
RgGuinier 3.7 nm
Dmax 10.3 nm
VolumePorod 186 nm3

SASDFF6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp complex

Beta sliding clampProbable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) experimental SAS data
DAMMIF model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) monomer, 33 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 15
RgGuinier 3.5 nm
Dmax 11.3 nm
VolumePorod 98 nm3

SASDFG6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex

Beta sliding clampProbable exodeoxyribonuclease III protein XthADNA ligase A experimental SAS data
DAMMIF model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 31 kDa Mycobacterium tuberculosis protein
DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 17
RgGuinier 5.8 nm
Dmax 25.3 nm
VolumePorod 501 nm3

SASDFH6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, 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
RgGuinier 5.8 nm
Dmax 19.1 nm
VolumePorod 496 nm3