Protein Family Models

Date:

2024-08-14

This family contains a number of putative eukaryotic acid phosphatases. Some family members represent the products of the PSI14 phosphatase family in Lycopersicon esculentum (Tomato) [1]. [1]. 11161030. Leps2, a phosphorus starvation-induced novel acid phosphatase from tomato. Baldwin JC, Karthikeyan AS, Raghothama KG;. Plant Physiol 2001;125:728-737. (from Pfam)

Date:

2024-10-16

This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2]. [1]. 8702766. Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. Hisano T, Hata Y, Fujii T, Liu JQ, Kurihara T, Esaki N, Soda K;. J Biol Chem 1996;271:20322-20330. [2]. 20485265. A mitochondrial phosphatase required for cardiolipin biosynthesis: the PGP phosphatase Gep4. Osman C, Haag M, Wieland FT, Brugger B, Langer T;. EMBO J. 2010;29:1976-1987 (from Pfam)

Date:

2024-10-16

MtnX family protein

Date:

2017-03-02

This HMM represents a subfamily of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. Subfamily IA, B, C and D are distinguished from the rest of the superfamily by the presence of a variable domain between the first and second conserved catalytic motifs. In subfamilies IA and IB, this domain consists of an alpha-helical bundle. It was necessary to model these two subfamilies separately, breaking them at a an apparent phylogenetic bifurcation, so that the resulting model(s) are not so broadly defined that members of subfamily III (which lack the variable domain) are included. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences.

Date:

2021-04-27

Members of this family are phosphatases from the HAD-IB family of superfamily of aspartate-nucleophile hydrolases. Members include MtnX, a 2,3-diketo-5-methylthio-1-phosphopentane phosphatase involved in a bacterial pathway for converting methylthioribose (MTR) to methionine. A more specific HMM, TIGR03333, identifies proteins that are MtnX per se.

Date:

2021-11-04