PDBsum entry 2c9c

Transcription regulation

PDB id

2c9c

Contents

			Protein chain

					245 a.a.

			Ligands

					ATP

			Metals

					_MG

			Waters ×144

References listed in PDB file

Key reference

Title

Structural basis of the nucleotide driven conformational changes in the aaa+ domain of transcription activator pspf.

Authors

M.Rappas, J.Schumacher, H.Niwa, M.Buck, X.Zhang.

Ref.

J Mol Biol, 2006, 357, 481-492. [DOI no: 10.1016/j.jmb.2005.12.052]

PubMed id

16430918

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Abstract

Bacterial enhancer-binding proteins (EBP) activate transcription by hydrolyzing ATP to restructure the sigma(54)-RNA polymerase-promoter complex. We compare six high resolution structures (<2.1 A) of the AAA(+) domain of EBP phage shock protein F (PspF) including apo, AMPPNP, Mg(2+)-ATP, and ADP forms. These structures permit a description of the atomic details underpinning the origins of the conformational changes occurring during ATP hydrolysis. Conserved regions of PspF's AAA(+) domain respond distinctively to nucleotide binding and hydrolysis, suggesting functional roles during the hydrolysis cycle, which completely agree with those derived from activities of PspF mutated at these positions. We propose a putative atomic switch that is responsible for coupling structural changes in the nucleotide-binding site to the repositioning of the sigma(54)-interacting loops. Striking similarities in nucleotide-specific conformational changes and atomic switch exist between PspF and the large T antigen helicase, suggesting conservation in the origin of those events amongst AAA(+) proteins.



	Figure 2. Figure 2. The nucleotide binding pocket of PspF[1-275] modelled on the structure of Click to view the MathML source- [0?wchp=dGLbVzb-zSkWA] . (a) Final 2F[o] -F[c] map of the Mg2+-ATP and surrounding water molecules at 2.1 Å resolution. The green arrow points to the Mg2+ and the dark green arrow points to the apical water molecule thought to be responsible for nucleophilic attack. (b) Details of the largely hydrophobic adenine ring binding pocket. The structures of apo (white), ATP (pink) and ADP (blue) are superposed and side-chains of residues involved in packing the purine base are shown as sticks. (c) Details of the interactions around the phosphate backbone. The R227 side-chain is modelled on the ATP-PspF[1-275] structure. Side-chains of residues of the Walker A motif (K42-E43), Walker B motif (D107-D108) and sensor II motif (R227, K230, N231) are shown as sticks in their different nucleotide states (apo in white, ATP in pink and ADP in blue). Also appearing as sticks are residues N64 and S62, responsible for relaying the conformational signal to L1. Hexa-coordination of the Mg2+ is highlighted by magenta dotted lines. The interactions surrounding the water molecule, thought to be responsible for the nucleophilic attack, are highlighted by yellow dotted lines.		Figure 5. Figure 5. Schematic representation of the proposed nucleotide-dependent relocation of L1 and L2 in EBP mediated through the atomic switch. For simplicity, we focus on the atomic switch and L1 and L2 loops within one subunit of the EBP hexamer. The GAFTGA motif is locked into an unfavourable conformation for s54 interaction in the ADP bound state as represented by ADP and ADP-NtrC1 structures (right). At the initial stage of hydrolysis as represented by ATP-PspF[1-275] structure, E108 stably interacts with N64, causing relocations of linker 1 and central b-sheet, affecting the network of interactions which coordinate GAFTGA containing L1 loop, ultimately releasing L1 loop for s54 interaction (left and bottom). At the point of ATP hydrolysis, the GAFTGA motif engages with s54 and L1 and L2 loops are stablized (top). Upon Pi release, the interaction between N64 and E108 breaks, allowing the GAFTGA motif to collapse and return to the ADP bound state (right).

PROCHECK

	Headers