Journal of Structural Biology 156 (2006) 190–199 www.elsevier.com/locate/yjsbi 1047-8477/$ - see front matter  2006 Elsevier Inc. All rights reserved. doi:10.1016/j.jsb.2006.01.006 Review Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation Jörg Schumacher a,¤ , Nicolas Joly a , Mathieu Rappas b , Xiaodong Zhang b , Martin Buck a a Division of Biology, Imperial College London, London, SW7 2AZ, UK b Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK Received 30 November 2005; received in revised form 16 January 2006; accepted 19 January 2006 Available online 20 February 2006 Abstract Initiation of transcription is a major point of transcriptional regulation and invariably involves the transition from a closed to an open RNA polymerase (RNAP) promoter complex. In the case of the  54 -RNAP, this multi step process requires energy, provided by ATP hydrolysis occurring within the AAA+ domain of enhancer binding proteins (EBPs). Typically, EBPs have an N-terminal regulatory domain, a central AAA+ domain that directly contacts  54 and a C-terminal DNA binding domain. The following AAA+ EBP crystal structures have recently become available: heptameric AAA+ domains of NtrC1 and dimeric NtrC1 with its regulatory domain, hexa- meric AAA+ domains of ZraR with DNA binding domains, apo and nucleotide bound forms of the AAA+ domain of PspF as well as a cryo-EM structure of the AAA+ domain of PspF complexed with  54 . These AAA+ domains reveal the structural conservation between EBPs and other AAA+ domains. EBP speciWc structural features involved in substrate remodelling are located proximal to the pore of the hexameric ring. Parallels with the substrate binding elements near the central pore of other AAA+ members are drawn. We propose a structural model of EBPs in complex with a  54 -RNAP-promoter complex.  2006 Elsevier Inc. All rights reserved. Keywords: AAA+ family; Enhancer binding proteins; Sigma54; Transcriptional activation; Energy coupling 1. Introduction Transcription is one of the fundamental processes in biology. The control of gene transcription is key to estab- lishing coordinated responses in a changing environment. Present in all kingdoms of life, RNA Polymerases (RNAP) are evolutionary conserved in sequence, structure, and function, although their precise subunit composition varies considerably between species (Ebright, 2000). Transcrip- tional regulation is most often achieved by control of tran- scriptional initiation. Transcription in bacteria is initiated by a RNAP isomerisation process in which the promoter DNA is melted close to the transcription start site (reviewed by Browning and Busby, 2004). Bacterial RNAP holoenzymes are composed of the  2 ' core enzyme associated with one of a range of sigma factors. Structures of several bacterial RNAPs have been solved by X-ray crys- tallography (reviewed by Murakami and Darst, 2003). The diVerent sigma factors confer promoter speciWcity and enable RNAP to distinguish between diVerent groups of promoters (Ishihama, 2000). Two diVerent classes of sigma factors are distinguished by sequence and mode of tran- scriptional initiation. The prototypical  70 type factors bind to promoter sequences at positions ¡35 and ¡10 from the transcription start site and transcriptional regulation is usually achieved by regulator proteins that recruit or obstruct  70 type RNAP to the promoter sites.  54 -RNAP is the major variant RNAP holoenzyme that binds to spe- ciWc promoter sequences at positions ¡24 (GG) and ¡12 (TGC) from the transcription start, where it remains in a closed conformation and is transcriptionally silent (Fig. 1) (Wigneshweraraj et al., 2005). The transition from a closed to an open RNAP-DNA promoter complex precedes * Corresponding author. Fax: +44 0 2075945419. E-mail address: j.schumacher@imperial.ac.uk (J. Schumacher).