Protein Family Models

This entry represents the N-terminal domain of XylR, an atypical AraC protein. This D-xylose-binding domain contains a periplasmic-binding protein (PBP) fold, similar to LacI/GalR transcription regulators, and mediates dimerization [1]. Paper describing PDB structure 4fe4. [1]. 23241389. Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain. Ni L, Tonthat NK, Chinnam N, Schumacher MA;. Nucleic Acids Res. 2013;41:1998-2008. (from Pfam)

Date:

2024-10-16

This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognises Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). (from Pfam)

Date:

2024-08-14

This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognises fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). (from Pfam)

Date:

2024-08-14

Date:

2024-08-14

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

Gene:

xylR

Date:

2023-07-01

XylR family transcriptional regulator similar to xylose operon transcription regulator XylR, a DNA transcription repressor that regulates the xylBAFGHR operon and contains an N-terminal periplasmic-binding protein (PBP) fold ligand binding domain and a C-terminal AraC-like DNA binding domain

Date:

2019-03-05