Protein Family Models

This entry represents the PKD domain of Dyslexia-associated protein KIAA0319-like protein, in which it is found in four copies. This entry also includes Kunitz-type protease inhibitor 1 and LRP11 from human. Paper describing PDB structure 2c26. [1]. 16314409. Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains. Najmudin S, Guerreiro CI, Carvalho AL, Prates JA, Correia MA, Alves VD, Ferreira LM, Romao MJ, Gilbert HJ, Bolam DN, Fontes CM;. J Biol Chem. 2006;281:8815-8828. Paper describing PDB structure 2y3u. [2]. 21947205. Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Eckhard U, Schonauer E, Nuss D, Brandstetter H;. Nat Struct Mol Biol. 2011;18:1109-1114. Paper describing PDB structure 2yhg. [3]. 21905122. Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism. Hehemann JH, Marsters C, Boraston AB;. Proteins. 2011;79:2992-2998. Paper describing PDB structure 2z4t. [4]. 17962295. Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition. Kakuta Y, Okino N, Kajiwara H, Ichikawa M, Takakura Y, Ito M, Yamamoto T;. Glycobiology. 2008;18:66-73. Paper describing PDB structure 4aqo. [5]. 23703618. Structural basis for activity regulation and substrate preference of clostridial collagenases G, H, and T. Eckhard U, Schonauer E, Brandstetter H;. J Biol Chem. 2013;288:20184-20194. (from Pfam)

Date:

2024-10-21

This FN3 like domain is found at the C-terminus of cucumisin proteins [1]. [1]. 22841692. Crystal structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L. Murayama K, Kato-Murayama M, Hosaka T, Sotokawauchi A, Yokoyama S, Arima K, Shirouzu M;. J Mol Biol. 2012;423:386-396. (from Pfam)

Date:

2024-10-16

This entry represents a wide variety of bacterial Ig domains. [1]. 21606337. Structure of a bacterial cell surface decaheme electron conduit. Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J, Reardon CL, Shi L, Beliaev AS, Marshall MJ, Wang Z, Watmough NJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ;. Proc Natl Acad Sci U S A. 2011;108:9384-9389. (from Pfam)

Date:

2024-10-16

This family includes the proteinase B inhibitor from Saccharomyces cerevisiae and the activation peptides from peptidases of the subtilisin family. The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of the mature peptidase [1], but have also been shown to act as 'temporary inhibitors' [2]. [1]. 7559646. Functional analysis of the propeptide of subtilisin E as an intramolecular chaperone for protein folding. Refolding and inhibitory abilities of propeptide mutants. Li Y, Hu Z, Jordan F, Inouye M;. J Biol Chem. 1995;270:25127-25132. [2]. 9247157. The propeptide of subtilisin BPN' as a temporary inhibitor and effect of an amino acid replacement on its inhibitory activity. Kojima S, Minagawa T, Miura K;. FEBS Lett. 1997;411:128-132. (from Pfam)

Date:

2024-10-16

The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor Swiss:O22925 and members of the RZF family Swiss:O43567. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors [1]. [1]. 11246007. The protease-associated domain: a homology domain associated with multiple classes of proteases. Luo X, Hofmann K;. Trends Biochem Sci 2001;26:147-148. (from Pfam)

Date:

2024-10-16

Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567. (from Pfam)

Date:

2024-08-14

This homology domain, GlyGly-CTERM, shares a species distribution with rhombosortase (TIGR03902), a subfamily of rhomboid-like intramembrane serine proteases. It is recognized, and cleaved, by rhombosortase. Shewanella species have the largest number of target proteins per genome, up to thirteen. The domain occurs at the extreme carboxyl-terminus of a diverse set of proteins, most of which are enzymes with conventional signal sequences and with hydrolytic activities: nucleases, proteases, agarases, etc. The agarase AgaA from Vibro sp. strain JT0107 is secreted into the medium, while the same protein heterologously expressed in E. coli is retained in the cell fraction. VesB, from Vibrio cholerae, was shown to be processed by rhombosortase so as to expose the second Gly of the motif, and then to be linked to a glycerophosphoethanolamine, prior to type II secretion. Note that both the processing, and the chemical structure of the domain (motif, hydrophobic predicted transmembrane helix, cluster of basic residues), closely parallels those of the LPXTG/sortase system, the PGF-CTERM/archaseosortase system, and the PEP-CTERM/exosortase(EpsH) system.

Date:

2023-07-12

S8 family peptidase is a subtilisin-like serine protease containing a Asp/His/Ser catalytic triad that is not homologous to trypsin

Date:

2022-11-14