Protein Family Models

This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam)

Date:

2024-08-14

This domain family is found in bacteria, archaea and eukaryotes, and is typically between 111 and 127 amino acids in length. The family is found in association with Pfam:PF04055. LAM catalyses the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine. [1]. 16166264. The x-ray crystal structure of lysine-2,3-aminomutase from. Clostridium subterminale.. Lepore BW, Ruzicka FJ, Frey PA, Ringe D;. Proc Natl Acad Sci U S A. 2005;102:13819-13824. (from Pfam)

Date:

2024-08-14

Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. [1]. 11222759. Radical SAM, a novel protein superfamily linking unresolved. steps in familiar biosynthetic pathways with radical mechanisms:. functional characterization using new analysis and information. visualization methods.. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE;. Nucleic Acids Res 2001;29:1097-1106.. [2]. 17335281. Anaerobic sulfatase-maturating enzymes: radical SAM enzymes able. to catalyze in vitro sulfatase post-translational modification.. Benjdia A, Leprince J, Guillot A, Vaudry H, Rabot S, Berteau O;. J Am Chem Soc. 2007;129:3462-3463.. [3]. 16766528. A new type of bacterial sulfatase reveals a novel maturation. pathway in prokaryotes.. Berteau O, Guillot A, Benjdia A, Rabot S;. J Biol Chem. 2006;281:22464-22470. (from Pfam)

Date:

2024-09-08

lys_2_3_AblA family protein

Date:

2017-03-02

This model describes lysine-2,3-aminomutase, which can occur in multiple pathways. It is designated AblA when paired with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. Lysine-2,3-aminomutase is belongs to lysine degradation pathways, where it is known as KamA. The enzyme belongs to the radical SAM superfamily.

Gene:

ablA

Date:

2023-08-28

This HMM represents essentially the whole of E. coli YjeK and of some of its apparent orthologs. YodO in Bacillus subtilis, a family member which is longer protein by an additional 100 residues, is characterized as a lysine 2,3-aminomutase with iron, sulphide and pyridoxal 5'-phosphate groups. The homolog MJ0634 from M. jannaschii is preceded by nearly 200 C-terminal residues. This family shows similarity to molybdenum cofactor biosynthesis protein MoaA and related proteins. Note that the E. coli homolog was expressed in E. coli and purified and found not to display display lysine 2,3-aminomutase activity. Active site residues are found in 100 residue extension in B. subtilis. Name changed to KamA family protein.

Date:

2021-05-12