Protein Family Models

This family contains Cass2 from Vibrio cholerae, an integron-associated protein that has been shown [1] to bind cationic drug compounds with submicromolar affinity. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species. [1]. 21390267. Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module. Deshpande CN, Harrop SJ, Boucher Y, Hassan KA, Di Leo R, Xu X, Cui H, Savchenko A, Chang C, Labbate M, Paulsen IT, Stokes HW, Curmi PM, Mabbutt BC;. PLoS One. 2011;6:e16934. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

This family contains the small molecule binding domain of a number of different bacterial transcription activators [1]. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding [3]. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira [3]. [1]. 10802742. Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Kwon HJ, Bennik MH, Demple B, Ellenberger T;. Nat Struct Biol 2000;7:424-430. [2]. 11948793. Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17. Romanowski MJ, Gibney SA, Burley SK;. Proteins 2002;47:403-407. [3]. 15281131. The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. Anantharaman V, Aravind L;. Proteins. 2004;56:795-807. (from Pfam)

Date:

2024-10-16

In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (Pfam:PF00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerisation domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilised when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added [1-2]. [1]. 9600836. Apo-AraC actively seeks to loop. Seabold RR, Schleif RF;. J Mol Biol 1998;278:529-538. [2]. 9600837. Arm-domain interactions in AraC. Saviola B, Seabold R, Schleif RF;. J Mol Biol 1998;278:539-548. (from Pfam)

Date:

2024-10-16

GyrI-like domain-containing protein adopts a beta-barrel fold similar to the effector-binding region of AraC/XylS transcription activators and may bind a small molecule; similar to Escherichia coli probable transcriptional regulator YgiV

Date:

2020-11-06