Protein Family Models

This domain is found at the C-terminus of hydrogenase small subunits including periplasmic [NiFeSe] hydrogenase small subunit, uptake hydrogenase small subunit and periplasmic [NiFe] hydrogenase small subunit. This C-terminal domain binds two of the three iron-sulfur clusters in this enzyme [1-3]. [1]. 20673834. The crystal structure of the [NiFe] hydrogenase from the. photosynthetic bacterium Allochromatium vinosum:. characterization of the oxidized enzyme (Ni-A state).. Ogata H, Kellers P, Lubitz W;. J Mol Biol. 2010;402:428-444.. [2]. 7854413. Crystal structure of the nickel-iron hydrogenase from. Desulfovibrio gigas.. Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M,. Fontecilla-Camps JC;. Nature 1995;373:580-587.. [3]. 10378275. The crystal structure of a reduced [NiFeSe] hydrogenase provides. an image of the activated catalytic center.. Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M,. Fontecilla-Camps JC;. Structure. 1999;7:557-566. (from Pfam)

Date:

2024-04-03

Date:

2023-12-12

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