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 occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, Pfam:PF04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin. [1]. 21478363. Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. Haft DH, Basu MK;. J Bacteriol. 2011;193:2745-2755. (from Pfam)

Date:

2024-10-16

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:

2024-10-16

PqqD and Radical_SAM domain-containing protein

Date:

2017-03-02

The SPASM domain usually occurs as a C-terminal extension to a radical SAM domain (see Pfam model PF04055)-containing protein, although some proteins with free-standing SPASM domains do occur. A radical SAM protein binds a 4Fe-4S cluster, and the SPASM domain binds two additional 4Fe-4S clusters. Radical SAM enzymes with an additional SPASM domain tend to be involved in protein modification. The acronym SPASM derives from the protein-modifying radical SAM enzymes of the Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin systems. Additional radical SAM/SPASM domain proteins participate in the maturation of quinohemoprotein amine dehydrogenase, the natural product Pep1357, SCIFF, sporulation killing factor, thurincin H, thuricin CD, etc. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. An incomplete SPASM domain that binds one 4Fe-4S cluster, instead of two, is called a TWITCH domain. This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model PF04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin.

Date:

2021-10-28