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Links from Protein

Items: 14

1.

GlgB N-terminal domain-containing protein

This is the N-terminal beta-sandwich domain of alpha-1,4-glucan branching enzyme GlgB and related proteins. This domain has a differential preference in substrate recognition and binding during amylase activity, when amylose is used as a substrate [2]. Paper describing PDB structure 1m7x. [1]. 12196524. The X-ray crystallographic structure of Escherichia coli branching enzyme. Abad MC, Binderup K, Rios-Steiner J, Arni RK, Preiss J, Geiger JH;. J Biol Chem. 2002;277:42164-42170. Paper describing PDB structure 3k1d. [2]. 20444687. Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity. Pal K, Kumar S, Sharma S, Garg SK, Alam MS, Xu HE, Agrawal P, Swaminathan K;. J Biol Chem. 2010;285:20897-20903. Paper describing PDB structure 4lpc. [3]. 26280198. Crystal Structures of Escherichia coli Branching Enzyme in Complex with Linear Oligosaccharides. Feng L, Fawaz R, Hovde S, Gilbert L, Chiou J, Geiger JH;. Biochemistry. 2015;54:6207-6218. Paper describing PDB structure 5e6y. [4]. 27139627. Crystal structures of Escherichia coli branching enzyme in complex with cyclodextrins. Feng L, Fawaz R, Hovde S, Sheng F, Nosrati M, Geiger JH;. Acta Crystallogr D Struct Biol. 2016;72:641-647. Paper describing PDB structure 5gqu. [5]. 28193843. Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model. Hayashi M, Suzuki R, Colleoni C, Ball SG, Fujita N, Suzuki E;. J Biol Chem. 2017;292:5465-5475. (from Pfam)

Date:
2024-10-29

Family Accession:
NF046567.1
Method:
HMM

2.

Carbohydrate-binding module 48 (Isoamylase N-terminal domain)

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)

GO Terms:
Molecular Function:
hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)
Biological Process:
carbohydrate metabolic process (GO:0005975)
Date:
2024-10-16

Family Accession:
NF014919.5
Method:
HMM

3.

alpha amylase C-terminal domain-containing protein

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)

GO Terms:
Molecular Function:
catalytic activity (GO:0003824)
Biological Process:
carbohydrate metabolic process (GO:0005975)
Molecular Function:
cation binding (GO:0043169)
Date:
2024-10-16

Family Accession:
NF014822.5
Method:
HMM

4.

alpha-amylase family glycosyl hydrolase

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)

GO Terms:
Molecular Function:
catalytic activity (GO:0003824)
Biological Process:
carbohydrate metabolic process (GO:0005975)
Date:
2024-10-16

Family Accession:
NF012356.5
Method:
HMM

5.
new record, indexing in progress
Family Accession:
6.
new record, indexing in progress
Family Accession:
7.
new record, indexing in progress
Family Accession:
8.
new record, indexing in progress
Family Accession:
9.
new record, indexing in progress
Family Accession:
10.
new record, indexing in progress
Family Accession:
11.

1,4-alpha-glucan-branching protein

1,4-alpha-glucan-branching protein transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain

Date:
2024-08-15

Family Accession:
11480855
Method:
Sparcle

12.

1,4-alpha-glucan branching protein GlgB

Catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain

Gene:
glgB
GO Terms:
Molecular Function:
1,4-alpha-glucan branching enzyme activity (GO:0003844)
Molecular Function:
hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)
Biological Process:
carbohydrate metabolic process (GO:0005975)
Biological Process:
glycogen biosynthetic process (GO:0005978)
Molecular Function:
cation binding (GO:0043169)
Date:
2021-08-24

Family Accession:
NF008967.0
Method:
HMM

13.

1,4-alpha-glucan branching enzyme

This HMM describes the glycogen branching enzymes which are responsible for the transfer of chains of approx. 7 alpha(1--4)-linked glucosyl residues to other similar chains (in new alpha(1--6) linkages) in the biosynthesis of glycogen. This enzyme is a member of the broader amylase family of starch hydrolases which fold as (beta/alpha)8 barrels, the so-called TIM-barrel structure [1,2]. All of the sequences comprising the seed of this model have been experimentally characterized. (For instance, [3]). This model encompasses both bacterial and eukaryotic species. No archaea have this enzyme, although Aquifex aolicus does. Two species, Bacillus thuringiensis and Clostridium perfringens have two sequences each which are annotated as amylases. These annotations are aparrently in error. GP|18143720 from C. perfringens, for instance, contains the note "674 aa, similar to gp:A14658_1 amylase (1,4-alpha-glucan branching enzyme (EC 2.4.1.18) ) from Bacillus thuringiensis (648 aa); 51.1% identity in 632 aa overlap." A branching enzyme from Porphyromonas gingivales, OMNI|PG1793, appears to be more closely related to the eukaryotic species (across a deep phylogenetic split) and may represent an instance of lateral transfer from this species' host. A sequence from Arabidopsis thaliana, GP|9294564, scores just above trusted, but appears either to contain corrupt sequence or, more likely, to be a pseudogene as some of the conserved catalytic residues common to the alpha amylase family are not conserved here.

Gene:
glgB
GO Terms:
Molecular Function:
1,4-alpha-glucan branching enzyme activity (GO:0003844)
Biological Process:
glycogen biosynthetic process (GO:0005978)
Date:
2021-04-27

Family Accession:
TIGR01515.1
Method:
HMM

14.

1,4-alpha-glucan branching protein GlgB

Catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain

Gene:
glgB
GO Terms:
Molecular Function:
1,4-alpha-glucan branching enzyme activity (GO:0003844)
Molecular Function:
hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)
Biological Process:
carbohydrate metabolic process (GO:0005975)
Biological Process:
glycogen biosynthetic process (GO:0005978)
Molecular Function:
cation binding (GO:0043169)
Date:
2021-07-22

Family Accession:
NF003811.1
Method:
HMM

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