Protein Family Models

Date:

2024-08-14

This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [1][2][3]. They are regulated by thiamine [2]. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor [4]. [1]. 12271461. Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Rodriguez-Navarro S, Llorente B, Rodriguez-Manzaneque MT, Ramne A, Uber G, Marchesan D, Dujon B, Herrero E, Sunnerhagen P, Perez-Ortin JE;. Yeast. 2002;19:1261-1276. [2]. 2358444. nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. Maundrell K;. J Biol Chem. 1990;265:10857-10864. [3]. 12777485. The THI5 gene family of Saccharomyces cerevisiae: distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine. Wightman R, Meacock PA;. Microbiology. 2003;149:1447-1460. [4]. 23048037. The last piece in the vitamin B1 biosynthesis puzzle: structural and functional insight into yeast 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase. Coquille S, Roux C, Fitzpatrick TB, Thore S;. J Biol Chem. 2012;287:42333-42343. (from Pfam)

Date:

2024-10-16

Many proteins that fold in the cytosol because a required cofactor is available there only, or because cytosolic chaperones assist in folding, or because high salt in the extracellular milieu would interfere with folding there, cannot rely on the standard general secretory (Sec) pathway for secretion across the plasma membrane. This model describes a family of predicted long, non-Sec signal sequences and signal-anchor sequences (uncleaved signal sequences). All contain a typically invariant pair of arginine residues, in a motif approximated by (S/T)-R-R-X-F-L-K, followed by a membrane-spanning hydrophobic region. The system that secretes pre-folded proteins with this motif is known as twin-arginine translocation, or TAT. Note that some variant forms, often lineage-specific ones such as the RKxFL version found in Leptospira, do occur but typically fall outside the scope of this HMM. Twin-arginine signal domains with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. The system, although far from universal in prokaryotes, is widespread in bacteria and present also in many archaea.

Date:

2019-11-27

ABC transporter substrate-binding protein functions as the initial receptor in the ABC transport of one of a variety of substrates, including ions such as bicarbonate and nitrate; belongs to the type 2 periplasmic binding protein (PBP2) family

Date:

2024-04-27