8URW

Cyanobacterial RNA polymerase elongation complex with NusG and CTP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase.

Qayyum, M.Z.Imashimizu, M.Leanca, M.Vishwakarma, R.K.Riaz-Bradley, A.Yuzenkova, Y.Murakami, K.S.

(2024) Proc Natl Acad Sci U S A 121: e2311480121-e2311480121

  • DOI: https://doi.org/10.1073/pnas.2311480121
  • Primary Citation of Related Structures:  
    8EMB, 8SYI, 8URW

  • PubMed Abstract: 

    Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spanning approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP in the absence of iNTP bound at the active site and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG, or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms and organelle.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
309Synechococcus elongatusMutation(s): 0 
Gene Names: rpoASynpcc7942_2209
EC: 2.7.7.6
UniProt
Find proteins for Q31L30 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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UniProt GroupQ31L30
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,100Synechococcus elongatusMutation(s): 0 
Gene Names: rpoBSynpcc7942_1522
EC: 2.7.7.6
UniProt
Find proteins for Q31N17 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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UniProt GroupQ31N17
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit gamma624Synechococcus elongatusMutation(s): 0 
Gene Names: rpoC1Synpcc7942_1523
EC: 2.7.7.6
UniProt
Find proteins for P42079 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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UniProt GroupP42079
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega76Synechococcus elongatusMutation(s): 0 
Gene Names: rpoZSynpcc7942_1710
EC: 2.7.7.6
UniProt
Find proteins for Q31MH9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'F [auth Z]1,318Synechococcus elongatusMutation(s): 0 
Gene Names: rpoC2Synpcc7942_1524
EC: 2.7.7.6
UniProt
Find proteins for Q31N15 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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UniProt GroupQ31N15
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusG205Synechococcus elongatusMutation(s): 0 
Gene Names: nusGSynpcc7942_0635
UniProt
Find proteins for Q31QK2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (40-MER)H [auth N]40synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (40-MER)I [auth T]40synthetic construct
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Entity ID: 9
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*AP*GP*AP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')J [auth R]21synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131860

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references