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TitleStructural basis for substrate binding and selection by human mitochondrial RNA polymerase.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 7134, Year 2024
Publish dateAug 20, 2024
AuthorsKarl Herbine / Ashok R Nayak / Dmitry Temiakov /
PubMed AbstractThe mechanism by which RNAP selects cognate substrates and discriminates between deoxy and ribonucleotides is of fundamental importance to the fidelity of transcription. Here, we present cryo-EM ...The mechanism by which RNAP selects cognate substrates and discriminates between deoxy and ribonucleotides is of fundamental importance to the fidelity of transcription. Here, we present cryo-EM structures of human mitochondrial transcription elongation complexes that reveal substrate ATP bound in Entry and Insertion Sites. In the Entry Site, the substrate binds along the O helix of the fingers domain of mtRNAP but does not interact with the templating DNA base. Interactions between RNAP and the triphosphate moiety of the NTP in the Entry Site ensure discrimination against nucleosides and their diphosphate and monophosphate derivatives but not against non-cognate rNTPs and dNTPs. Closing of the fingers domain over the catalytic site results in delivery of both the templating DNA base and the substrate into the Insertion Site and recruitment of the catalytic magnesium ions. The cryo-EM data also reveal a conformation adopted by mtRNAP to reject a non-cognate substrate from its active site. Our findings establish a structural basis for substrate binding and suggest a unified mechanism of NTP selection for single-subunit RNAPs.
External linksNat Commun / PubMed:39164235 / PubMed Central
MethodsEM (single particle)
Resolution2.54 - 2.9 Å
Structure data

42027

8u8u

EMDB-42027, PDB-8u8u:
Cryo-EM Structure of Cognate Substrate ATP Bound in the Entry Site (ES) of Human Mitochondrial Transcription Elongation Complex
Method: EM (single particle) / Resolution: 2.9 Å

42028

8u8v

EMDB-42028, PDB-8u8v:
Cryo-EM structure of Substrate ATP Bound in the Insertion Site (IS) of Human Mitochondrial Transcription Elongation Complex
Method: EM (single particle) / Resolution: 2.74 Å

44448

9bdc

EMDB-44448, PDB-9bdc:
Cryo-EM Structure of the TEFM bound Human Mitochondrial Transcription Elongation Complex in a Closed Fingers Domain Conformation
Method: EM (single particle) / Resolution: 2.54 Å

44449

9bdd

EMDB-44449, PDB-9bdd:
Cryo-EM Structure of Non-Cognate Substrate Bound in the Entry Site (ES) of Human Mitochondrial Transcription Elongation Complex
Method: EM (single particle) / Resolution: 2.86 Å

Chemicals

ChemComp-APC:
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / AMP-CPP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSCRIPTION/DNA/RNA / Mitochondrial RNA Polymerase / Nucleotide Selection / Nucleotide Discrimination / TRANSCRIPTION / Protein-RNA-DNA Complex / POLRMT / TRANSCRIPTION-DNA-RNA complex / TEFM

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