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TitleMechanistic understanding of UvrA damage detection and lesion hand-off to UvrB in Nucleotide Excision Repair.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 3416, Year 2025
Publish dateApr 10, 2025
AuthorsMarianna Genta / Giulia Ferrara / Riccardo Capelli / Diego Rondelli / Sarah Sertic / Martino Bolognesi / Menico Rizzi / Franca Rossi / David Jeruzalmi / Antonio Chaves-Sanjuan / Riccardo Miggiano /
PubMed AbstractNucleotide excision repair (NER) represents one of the major molecular machineries that control chromosome stability in all living species. In Eubacteria, the initial stages of the repair process are ...Nucleotide excision repair (NER) represents one of the major molecular machineries that control chromosome stability in all living species. In Eubacteria, the initial stages of the repair process are carried out by the UvrABC excinuclease complex. Despite the wealth of structural data available, some crucial details of the pathway remain elusive. In this study, we present a structural investigation of the Mycobacterium tuberculosis UvrAUvrB complex and of the UvrA dimer, both in complex with damaged DNA. Our analyses yield insights into the DNA binding mode of UvrA, showing an unexplored conformation of Insertion Domains (IDs), underlying the essential role of these domains in DNA coordination. Furthermore, we observe an interplay between the ID and the UvrB Binding Domain (UBD): after the recognition of the damage, the IDs repositions with the concomitant reorganization of UBD, allowing the formation of the complex between UvrA and UvrB. These events are detected along the formation of the uncharacterized UvrAUvrB-DNA and the UvrAUvrB-DNA complexes which we interpret as hierarchical steps initiating the DNA repair cascade in the NER pathway, resulting in the formation of the pre-incision complex.
External linksNat Commun / PubMed:40210888 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 4.9 Å
Structure data

EMDB-51168: MtUvrA2 bound to endogenous E. coli DNA at low resolution
Method: EM (single particle) / Resolution: 4.2 Å

51169

9ga2

EMDB-51169, PDB-9ga2:
MtUvrA2 dimer empty
Method: EM (single particle) / Resolution: 4.9 Å

51170

9ga3

EMDB-51170, PDB-9ga3:
MtUvrA2UvrB bound to damaged oligonucleotide
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-51171: MtUvrA2UvrB2 bound to damaged oligonucleotide (half 1)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-51172: MtUvrA2UvrB2 bound to damaged oligonucleotide (half 2)
Method: EM (single particle) / Resolution: 3.7 Å

51173

9ga4

EMDB-51173: Composite map of MtUvrA2UvrB2-DNA
PDB-9ga4: MtUvrA2UvrB2 bound to damaged oligonucleotide
Method: EM (single particle) / Resolution: 3.7 Å

51174

9ga5

EMDB-51174, PDB-9ga5:
MtUvrA2 bound to endogenous E. coli DNA
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-51220: Consensus map of MtUvrA2UvrB2-DNA
Method: EM (single particle) / Resolution: 3.7 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • mycobacterium tuberculosis (bacteria)
  • escherichia coli (E. coli)
KeywordsDNA BINDING PROTEIN / DNA repair / NER / UVRA / UVRB / UVR / MTB

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