Isoamylase
Isoamylase (glycogen 6-glucanohydrolase, EC 3.2.1.68) is one of the starch-debranching enzymes that catalyses the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen. Belongs to Glycoside Hydrolase Family 13.
Reference Protein and Structure
- Sequence
-
P10342
(3.2.1.68)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Pseudomonas amyloderamosa (Bacteria)
- PDB
-
1bf2
- STRUCTURE OF PSEUDOMONAS ISOAMYLASE
(2.0 Å)
- Catalytic CATH Domains
-
3.20.20.80
2.60.40.10
(see all for 1bf2)
- Cofactors
- Calcium(2+) (1)
Enzyme Reaction (EC:3.2.1.68)
+
→
+
Alternative enzyme names: Debranching enzyme, Glycogen alpha-1,6-glucanohydrolase,
Enzyme Mechanism
Introduction
Asp375 initiates a nucleophilic attack on the substrate, eliminating one of the products. A water molecule is then activated by Glu435 and attacks the enzyme-substrate complex, eliminating the second product and regenerating the enzyme active site.
Catalytic Residues Roles
| UniProt | PDB* (1bf2) | ||
| Asp401 | Asp375A | Acts as the catalytic nucleophile. | covalent catalysis |
| Glu461 | Glu435A | Acts as the general acid/base. | proton shuttle (general acid/base) |
| Asp536 | Asp510A | Acts as a transition state stabiliser. | transition state stabiliser |
| Asn258, Glu255, Thr256 (main-C), Asp285, Asp154 | Asn232A, Glu229A, Thr230A (main-C), Asp259A, Asp128A | Forms calcium binding site. | metal ligand |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Abad MC et al. (2002), J Biol Chem, 277, 42164-42170. The X-ray Crystallographic Structure ofEscherichia coli Branching Enzyme. DOI:10.1074/jbc.m205746200. PMID:12196524.
- Noguchi J et al. (2011), Glycobiology, 21, 1108-1116. Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding. DOI:10.1093/glycob/cwr049. PMID:21493662.
- Katsuya Y et al. (1998), J Mol Biol, 281, 885-897. Three-dimensional structure of Pseudomonas isoamylase at 2.2 Å resolution 1 1Edited by R. Huber. DOI:10.1006/jmbi.1998.1992. PMID:9719642.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp128A | metal ligand |
| Glu229A | metal ligand |
| Thr230A (main-C) | metal ligand |
| Asn232A | metal ligand |
| Asp259A | metal ligand |
| Asp375A | covalent catalysis |
| Glu435A | proton shuttle (general acid/base) |
| Asp510A | transition state stabiliser |