Protein Family Models

This is a family of bacterial and eukaryotic proteins that belong to the Cupin superfamily. Some of the proteins in this family are annotated as being members of the AraC family of transcription factors, in which case this domain corresponds to the ligand binding domain. (from Pfam)

Date:

2024-08-14

Date:

2024-08-14

This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). [1]. 9573603. Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. Dunwell JM;. Biotechnol Genet Eng Rev 1998;15:1-32. (from Pfam)

Date:

2024-10-16

This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerisation found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity [1]. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins [2]. This domain is also found in (S)-ureidoglycine aminohydrolase (UGlyAH) from E.coli, which is involved in the anaerobic nitrogen utilisation via the assimilation of allantoin. It catalyses the deamination of allantoin to produce S-ureidoglycolate and ammonia from S-ureidoglycine [3,4]. [1]. 26448059. The EutQ and EutP proteins are novel acetate kinases involved in ethanolamine catabolism: physiological implications for the function of the ethanolamine metabolosome in Salmonella enterica. Moore TC, Escalante-Semerena JC;. Mol Microbiol. 2016;99:497-511. [2]. 23144756. Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment. Pitts AC, Tuck LR, Faulds-Pain A, Lewis RJ, Marles-Wright J;. PLoS One. 2012;7:e48360. [3]. 19935661. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Werner AK, Romeis T, Witte CP;. Nat Chem Biol. 2010;6:19-21. [4]. 20038185. Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. Serventi F, Ramazzina I, Lamberto I, Puggioni V, Gatti R, Percudani R;. ACS Chem Biol. 2010;5:203-214. (from Pfam)

Date:

2024-10-16

This family represents the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif Pfam:PF00165. This domain is distantly related to the Cupin domain Pfam:PF00190. [1]. 9103202. Structural basis for ligand-regulated oligomerization of AraC. Soisson SM, MacDougall-Shackleton B, Schleif R, Wolberger C;. Science 1997;276:421-425. (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

AraC family transcriptional regulator containing a cupin domain as its effector domain and an AraC family helix-turn-helix (HTH) DNA binding domain, controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

Date:

2024-09-19