Protein Family Models

Date:

2024-08-14

This is the N-terminal domain found in debranching enzyme such as Pullulanase (PulA)from Anoxybacillus sp. LM18-11. The PulA structure comprises four domains (N1, N2, A, and C). This is the N1 domain which has been identified as a carbohydrate-binding motif. Two maltotriose or maltotetraose molecules were found between the N1 domain and a loop of the A domain in the PulA-maltotriose or PulA-maltotetraose structures. These carbohydrates are bound in a parallel binding mode close to each other and form hydrogen bonds. The sugar moieties bound to the N1 domain are not immediately adjacent to the active site, but the enzyme might use N1 binding to attract and grab the substrate. Functional analysis indicate that N1 is important for catalytic activity and thermostability in addition to assisting substrate binding. The structure of the N1 domain reveals a classic distorted beta-jelly roll fold consisting of two anti-parallel beta-sheets, forming a concave and a convex surface. On the concave side of N1 domain there is a cleft to accommodate two molecules of maltotriose or maltotetraose [1]. [1]. 24375572. Functional and structural studies of pullulanase from. Anoxybacillus sp. LM18-11.. Xu J, Ren F, Huang CH, Zheng Y, Zhen J, Sun H, Ko TP, He M, Chen. CC, Chan HC, Guo RT, Song H, Ma Y;. Proteins. 2014;82:1685-1693. (from Pfam)

Date:

2024-08-14

This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase. [1]. 9719642. Three-dimensional structure of Pseudomonas isoamylase at 2.2 A. resolution.. Katsuya Y, Mezaki Y, Kubota M, Matsuura Y;. J Mol Biol 1998;281:885-897.. [2]. 14673168. Mutations in the gal83 glycogen-binding domain activate the. snf1/gal83 kinase pathway by a glycogen-independent mechanism.. Wiatrowski HA, Van Denderen BJ, Berkey CD, Kemp BE, Stapleton D,. Carlson M;. Mol Cell Biol 2004;24:352-361.. [3]. 12747837. AMPK beta subunit targets metabolic stress sensing to glycogen.. Polekhina G, Gupta A, Michell BJ, van Denderen B, Murthy S, Feil. SC, Jennings IG, Campbell DJ, Witters LA, Parker MW, Kemp BE,. Stapleton D;. Curr Biol 2003;13:867-871.. [4]. 12747836. A novel domain in AMP-activated protein kinase causes glycogen. storage bodies similar to those seen in hereditary cardiac. arrhythmias.. Hudson ER, Pan DA, James J, Lucocq JM, Hawley SA, Green KA, Baba. O, Terashima T, Hardie DG;. Curr Biol 2003;13:861-866. (from Pfam)

Date:

2024-08-14

Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain. [1]. 8107092. Refined molecular structure of pig pancreatic alpha-amylase at. 2.1 A resolution.. Larson SB, Greenwood A, Cascio D, Day J, McPherson A;. J Mol Biol 1994;235:1560-1584.. [2]. 9600843. Crystal structure of yellow meal worm alpha-amylase at 1.64 A. resolution.. Strobl S, Maskos K, Betz M, Wiegand G, Huber R, Gomis-Ruth FX,. Glockshuber R;. J Mol Biol 1998;278:617-628. (from Pfam)

Date:

2024-08-14

Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the subfamilies described in TIGR02102 and TIGR02103 but having a different domain architecture with shorter sequences. Members are called type I pullulanases.

Gene:

pulA

Date:

2021-04-27