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

This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila. A sequence-related jojoba acyl CoA reductase is also included. [1]. 9351246. The Arabidopsis MALE STERILITY 2 protein shares similarity with. reductases in elongation/condensation complexes.. Aarts MG, Hodge R, Kalantidis K, Florack D, Wilson ZA, Mulligan. BJ, Stiekema WJ, Scott R, Pereira A;. Plant J 1997;12:615-623. (from Pfam)

Date:

2024-08-14

This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions. [1]. 9174344. Structural analysis of UDP-sugar binding to UDP-galactose. 4-epimerase from Escherichia coli.. Thoden JB, Hegeman AD, Wesenberg G, Chapeau MC, Frey PA, Holden. HM;. Biochemistry 1997;36:6294-6304. (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

Date:

2024-08-14

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

This model describes a thioester reductase domain that occurs invariably at the C-terminus of proteins that contain it. Most proteins with the domain are non-ribosomal peptide synthetases (NRPS), but the domain also occurs in some polyketide synthases (PKS). The domain participates in biosynthetic pathways in which substrate is activated by adenylation, then transferred as a thioester to a protein's covalently linked pantetheine cofactor. The thioester bond is then reduced, breaking the bond to release the product, and to regenerate the pantetheine thiol (PMID:11254122). Examples of this domain include the terminal domain from the fungal alpha aminoadipate reductase enzyme (also known as aminoadipate semialdehyde dehydrogenase) which is involved in the biosynthesis of lysine (PMID:10320345), as well as the reductase-containing component of the myxochelin biosynthetic gene cluster, MxcG (PMID:11029592). The activity of this domain is fundamentally different from the more common beta-ketoreductase domains of PKS, which act at a carbonyl two carbons removed from the thioester and form an alcohol as a product.

Date:

2022-03-28