5D4C

Crystal structure of Thermus thermophilus product complex for transcription initiation with ATP and CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.

Bird, J.G.Zhang, Y.Tian, Y.Panova, N.Barvik, I.Greene, L.Liu, M.Buckley, B.Krasny, L.Lee, J.K.Kaplan, C.D.Ebright, R.H.Nickels, B.E.

(2016) Nature 535: 444-447

  • DOI: 10.1038/nature18622
  • Primary Citation of Related Structures:  
    5D4D, 5D4C, 5D4E

  • PubMed Abstract: 
  • The chemical nature of the 5′ end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency, and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation. Recently it has been shown that some bacterial RNA species carry a 5′-end structure reminiscent of the 5′ 7-methylguanylate ‘cap’ in eukaryotic RNA ...

    The chemical nature of the 5′ end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency, and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation. Recently it has been shown that some bacterial RNA species carry a 5′-end structure reminiscent of the 5′ 7-methylguanylate ‘cap’ in eukaryotic RNA. In particular, RNA species containing a 5′-end nicotinamide adenine dinucleotide (NAD+) or 3′-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria. It has been proposed that NAD+, reduced NAD+ (NADH) and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps. Here we show instead that NAD+, NADH and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated ‘ab initio capping’ may occur in all organisms.


    Organizational Affiliation

    The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, University of Tromsø, Tromsø, Norway. kirsti.leiros@uit.no



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha ABKL315Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q5SHR6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHR6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta CM1119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoBTTHA1813
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta' DN1524Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoCTTHA1812
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE8
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega EO99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoZTTHA1561
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE7
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA FP443Thermus thermophilus HB8Mutation(s): 0 
Gene Names: sigATTHA0532
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 6
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3')G, R19Thermus thermophilus
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 7
    MoleculeChainsLengthOrganismImage
    DNA (27-MER)H, S27Thermus thermophilus
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ATP
    Query on ATP

    Download Ideal Coordinates CCD File 
    D, N
    ADENOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O13 P3
    ZKHQWZAMYRWXGA-KQYNXXCUSA-N
     Ligand Interaction
    CTP
    Query on CTP

    Download Ideal Coordinates CCD File 
    D, N
    CYTIDINE-5'-TRIPHOSPHATE
    C9 H16 N3 O14 P3
    PCDQPRRSZKQHHS-XVFCMESISA-N
     Ligand Interaction
    C
    Query on C

    Download Ideal Coordinates CCD File 
    D, N
    CYTIDINE-5'-MONOPHOSPHATE
    C9 H14 N3 O8 P
    IERHLVCPSMICTF-XVFCMESISA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    D, N
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    B, D, F, K, L, N, P
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.28 Å
    • R-Value Free: 0.257 
    • R-Value Work: 0.211 
    • R-Value Observed: 0.214 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 185.96α = 90
    b = 103.64β = 98.3
    c = 297.42γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data collection
    SCALEPACKdata scaling
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2016-07-06
      Type: Initial release
    • Version 1.1: 2016-07-20
      Changes: Database references
    • Version 1.2: 2016-07-27
      Changes: Database references
    • Version 1.3: 2016-08-03
      Changes: Database references
    • Version 1.4: 2016-10-12
      Changes: Source and taxonomy