6ZXM

Diguanylate cyclase DgcR in complex with c-di-GMP

Summary for 6ZXM

• Entry DOI: 10.2210/pdb6zxm/pdb
• Descriptor: Putative GGDEF/response regulator receiver domain protein, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one), MAGNESIUM ION (3 entities in total)
• Functional Keywords: ggdef domain, receiver domain, rec, c-di-gmp, leptospira, signaling protein
• Biological source: Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
• Total number of polymer chains: 6
• Total formula weight: 224977.35

Authors

Teixeira, R.D.,Schirmer, T. (deposition date: 2020-07-29, release date: 2021-03-31, Last modification date: 2024-01-31)

Primary citation

Teixeira, R.D.,Holzschuh, F.,Schirmer, T.
Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase.
Nat Commun, 12:2162-2162, 2021

PubMed Abstract: Diguanylate cyclases synthesising the bacterial second messenger c-di-GMP are found to be regulated by a variety of sensory input domains that control the activity of their catalytical GGDEF domain, but how activation proceeds mechanistically is, apart from a few examples, still largely unknown. As part of two-component systems, they are activated by cognate histidine kinases that phosphorylate their Rec input domains. DgcR from Leptospira biflexa is a constitutively dimeric prototype of this class of diguanylate cyclases. Full-length crystal structures reveal that BeF pseudo-phosphorylation induces a relative rotation of two rigid halves in the Rec domain. This is coupled to a reorganisation of the dimeric structure with concomitant switching of the coiled-coil linker to an alternative heptad register. Finally, the activated register allows the two substrate-loaded GGDEF domains, which are linked to the end of the coiled-coil via a localised hinge, to move into a catalytically competent dimeric arrangement. Bioinformatic analyses suggest that the binary register switch mechanism is utilised by many diguanylate cyclases with N-terminal coiled-coil linkers.

PubMed: 33846343
DOI: 10.1038/s41467-021-22492-7

Experimental method

X-RAY DIFFRACTION (3.3 Å)