Protein Family Models

This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices. (from Pfam)

Date:

2024-08-14

A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine. (from Pfam)

Date:

2024-08-14

Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa. [1]. 9560421. Genetic evidence for a role of thioesterase domains, integrated. in or associated with peptide synthetases, in non-ribosomal. peptide biosynthesis in Bacillus subtilis.. Schneider A, Marahiel MA;. Arch Microbiol 1998;169:404-410. (from Pfam)

Date:

2024-08-14

This domain is found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non- ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (Pfam:PF00550). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site [1]. [1]. 9712910. Peptide bond formation in nonribosomal peptide biosynthesis.. Catalytic role of the condensation domain.. Stachelhaus T, Mootz HD, Bergendahl V, Marahiel MA;. J Biol Chem 1998;273:22773-22781. (from Pfam)

Date:

2024-08-14

Date:

2024-08-14

Transfers D-alanine to the D-alanyl carrier protein during the incorporation of D-alanine into lipoteichoic acid

Gene:

dltA

Date:

2020-10-26

This domain appears to be located immediately downstream from a condensation domain (PF00668), and is followed primarily by the end of the molecule or another condensation domain (in a few cases it is followed by PF00501, an AMP-binding module). The converse is not true, PF00668 domains are not always followed by this domain. This implicates this domain in possible post-condensation modification events. This HMM is 171 amino acids long and contains three very highly conserved regions. At the N-terminus is a nearly invariant lysine (position 11) followed by xxxRxxPxxGxGYG in which the proline and the first glycine are invariant. This is followed approximately 22 residues later by the motif FNYLG. Near the C-terminus of the domain is the sequence TxSD where the serine and aspartate are nearly invariant.

Date:

2019-09-10

This model represents a domain responsible for the specific recognition of amino acids and activation as adenylyl amino acids. The reaction catalyzed is aa + ATP -> aa-AMP + PPi. These domains are usually found as components of multi-domain non-ribosomal peptide synthetases and are usually called "A-domains" in that context (for a review, see [1]). A-domains are almost invariably followed by "T-domains" (thiolation domains, PF00550) to which the amino acid adenylate is transferred as a thiol-ester to a bound pantetheine cofactor with the release of AMP (these are also called peptide carrier proteins, or PCPs. When the A-domain does not represent the first module (corresponding to the first amino acid in the product molecule) it is usually preceded by a "C-domain" (condensation domain, PF00668) which catalyzes the ligation of two amino acid thiol-esters from neighboring modules. This domain is a subset of the AMP-binding domain found in Pfam (PF00501) which also hits substrate--CoA ligases and luciferases. Sequences scoring in between trusted and noise for this model may be ambiguous as to whether they activate amino acids or other molecules lacking an alpha amino group.

Date:

2022-02-08