5D4Z

Crystal structure of Repressor from Salmonella-temperate phage

Summary for 5D4Z

• Entry DOI: 10.2210/pdb5d4z/pdb
• Related: 5D50
• Descriptor: Repressor (2 entities in total)
• Functional Keywords: repressor, dna binding protein
• Biological source: Salmonella phage SPC32H
• Total number of polymer chains: 32
• Total formula weight: 376304.70

Authors

Kim, H.J.,Yoon, H.J.,Ryu, S.,Lee, H.H. (deposition date: 2015-08-10, release date: 2016-04-27, Last modification date: 2023-11-08)

Primary citation

Kim, M.,Kim, H.J.,Son, S.H.,Yoon, H.J.,Lim, Y.,Lee, J.W.,Seok, Y.-J.,Jin, K.S.,Yu, Y.G.,Kim, S.K.,Ryu, S.,Lee, H.H.
Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor
Proc.Natl.Acad.Sci.USA, 113:E2480-E2488, 2016

PubMed Abstract: DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92-198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant.

PubMed: 27099293
DOI: 10.1073/pnas.1602618113

Experimental method

X-RAY DIFFRACTION (2.98 Å)