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

doi: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

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

Biochemistry & Molecular Biology

Research output: Contribution to journal › Article › peer-review

63 Scopus citations

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-BeF_x (ground-state mimics), ADP-AlF_x (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-BeF_x state, and from the ADP-AlF_x state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to σ54, with ADP-AlF_x 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 language	English (US)
Pages (from-to)	429-440
Number of pages	12
Journal	Structure
Volume	15
Issue number	4
DOIs	https://doi.org/10.1016/j.str.2007.02.007
State	Published - Apr 2007

All Science Journal Classification (ASJC) codes

Structural Biology
Molecular Biology

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10.1016/j.str.2007.02.007

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@article{621b046946dd489695fa40d5701d41f7,

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

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}",

note = "Funding Information: We thank Dmitri Svergun and Maxim Petoukhov for advice and modifying GASBOR to accommodate P7 symmetry, and Sydney Kustu for making useful comments on the manuscript. This work was funded by NSF, Huck Institute (Penn State), and NIH grants to B.T.N., an NIH grant to D.E.W., and a DOE grant to E.N. and B.T.N. E.N. is a Howard Hughes Medical Institute Investigator. Use of the Advanced Photon Source was supported by the DOE under contract number W-31-109-ENG-38, and the BioCAT is an NIH-supported research center. ",

year = "2007",

month = apr,

doi = "10.1016/j.str.2007.02.007",

language = "English (US)",

volume = "15",

pages = "429--440",

journal = "Structure",

issn = "0969-2126",

publisher = "Cell Press",

number = "4",

}

TY - JOUR

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

N1 - Funding Information: We thank Dmitri Svergun and Maxim Petoukhov for advice and modifying GASBOR to accommodate P7 symmetry, and Sydney Kustu for making useful comments on the manuscript. This work was funded by NSF, Huck Institute (Penn State), and NIH grants to B.T.N., an NIH grant to D.E.W., and a DOE grant to E.N. and B.T.N. E.N. is a Howard Hughes Medical Institute Investigator. Use of the Advanced Photon Source was supported by the DOE under contract number W-31-109-ENG-38, and the BioCAT is an NIH-supported research center.

PY - 2007/4

Y1 - 2007/4

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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JO - Structure

JF - Structure

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ER -

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

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