ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54

Baoyu Chen, Michaeleen Doucleff, David E. Wemmer, Sacha De Carlo, Hector H. Huang, Eva Nogales, Timothy R. Hoover, Elena Kondrashkina, Liang Guo, B. Tracy Nixon

Research output: Contribution to journalArticle

59 Citations (Scopus)

Abstract

Transcription initiation by the σ54 form of bacterial RNA polymerase requires hydrolysis of ATP by an enhancer binding protein (EBP). We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeFx (ground-state mimics), ADP-AlFx (a transition-state mimic), or ADP (product) show substantial changes in the position of the GAFTGA loops that contact polymerase, particularly upon conversion from the apo state to the ADP-BeFx state, and from the ADP-AlFx state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to σ54, with ADP-AlFx having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and σ54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.

Original languageEnglish (US)
Pages (from-to)429-440
Number of pages12
JournalStructure
Volume15
Issue number4
DOIs
StatePublished - Apr 1 2007

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Adenosine Diphosphate
Adenosine Triphosphatases
Adenosine Triphosphate
Proteins
Carrier Proteins
Hydrolysis
Bacterial RNA
Adenylyl Imidodiphosphate
DNA-Directed RNA Polymerases
Nucleotides
Phosphates

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Chen, Baoyu ; Doucleff, Michaeleen ; Wemmer, David E. ; De Carlo, Sacha ; Huang, Hector H. ; Nogales, Eva ; Hoover, Timothy R. ; Kondrashkina, Elena ; Guo, Liang ; Nixon, B. Tracy. / ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54. In: Structure. 2007 ; Vol. 15, No. 4. pp. 429-440.
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abstract = "Transcription initiation by the σ54 form of bacterial RNA polymerase requires hydrolysis of ATP by an enhancer binding protein (EBP). We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeFx (ground-state mimics), ADP-AlFx (a transition-state mimic), or ADP (product) show substantial changes in the position of the GAFTGA loops that contact polymerase, particularly upon conversion from the apo state to the ADP-BeFx state, and from the ADP-AlFx state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to σ54, with ADP-AlFx having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and σ54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.",
author = "Baoyu Chen and Michaeleen Doucleff and Wemmer, {David E.} and {De Carlo}, Sacha and Huang, {Hector H.} and Eva Nogales and Hoover, {Timothy R.} and Elena Kondrashkina and Liang Guo and Nixon, {B. Tracy}",
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Chen, B, Doucleff, M, Wemmer, DE, De Carlo, S, Huang, HH, Nogales, E, Hoover, TR, Kondrashkina, E, Guo, L & Nixon, BT 2007, 'ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54', Structure, vol. 15, no. 4, pp. 429-440. https://doi.org/10.1016/j.str.2007.02.007

ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54. / Chen, Baoyu; Doucleff, Michaeleen; Wemmer, David E.; De Carlo, Sacha; Huang, Hector H.; Nogales, Eva; Hoover, Timothy R.; Kondrashkina, Elena; Guo, Liang; Nixon, B. Tracy.

In: Structure, Vol. 15, No. 4, 01.04.2007, p. 429-440.

Research output: Contribution to journalArticle

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T1 - ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54

AU - Chen, Baoyu

AU - Doucleff, Michaeleen

AU - Wemmer, David E.

AU - De Carlo, Sacha

AU - Huang, Hector H.

AU - Nogales, Eva

AU - Hoover, Timothy R.

AU - Kondrashkina, Elena

AU - Guo, Liang

AU - Nixon, B. Tracy

PY - 2007/4/1

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N2 - Transcription initiation by the σ54 form of bacterial RNA polymerase requires hydrolysis of ATP by an enhancer binding protein (EBP). We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeFx (ground-state mimics), ADP-AlFx (a transition-state mimic), or ADP (product) show substantial changes in the position of the GAFTGA loops that contact polymerase, particularly upon conversion from the apo state to the ADP-BeFx state, and from the ADP-AlFx state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to σ54, with ADP-AlFx having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and σ54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.

AB - Transcription initiation by the σ54 form of bacterial RNA polymerase requires hydrolysis of ATP by an enhancer binding protein (EBP). We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeFx (ground-state mimics), ADP-AlFx (a transition-state mimic), or ADP (product) show substantial changes in the position of the GAFTGA loops that contact polymerase, particularly upon conversion from the apo state to the ADP-BeFx state, and from the ADP-AlFx state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to σ54, with ADP-AlFx having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and σ54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.

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