PDBsum entry 1fa2

Hydrolase

PDB id

1fa2

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Contents

			Protein chain

					498 a.a. *

			Ligands

					RR7-GLC


					DTT

			Waters ×138

* Residue conservation analysis

PDB id:

1fa2

Links

Name:

Hydrolase

Title:

Crystal structure of beta-amylase from sweet potato

Structure:

Beta-amylase. Chain: a. Ec: 3.2.1.2

Source:

Ipomoea batatas. Sweet potato. Organism_taxid: 4120

Biol. unit:

Dimer (from PDB file)

Resolution:

2.30Å

R-factor:

0.213

R-free:

0.281

Authors:

B.I.Lee,C.G.Cheong,S.W.Suh

Key ref:

C.G.Cheong et al. (1995). Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato. Proteins, 21, 105-117. PubMed id: 7777485

Date:

12-Jul-00

Release date:

16-Aug-00

PROCHECK

	Headers

	References

Protein chain

P10537 (AMYB_IPOBA) - Beta-amylase from Ipomoea batatas

Seq: Struc:					499 a.a. 498 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.3.2.1.2 - beta-amylase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.

	Proteins 21:105-117 (1995)
PubMed id: 7777485

Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato.
C.G.Cheong, S.H.Eom, C.Chang, D.H.Shin, H.K.Song, K.Min, J.H.Moon, K.K.Kim, K.Y.Hwang, S.W.Suh.

ABSTRACT

Sweet potato beta-amylase is a tetramer of identical subunits, which are arranged to exhibit 222 molecular symmetry. Its subunit consists of 498 amino acid residues (Mr 55,880). It has been crystallized at room temperature using polyethylene glycol 1500 as precipitant. The crystals, growing to dimensions of 0.4 mm x 0.4 mm x 1.0 mm within 2 weeks, belong to the tetragonal space group P4(2)2(1)2 with unit cell dimensions of a = b = 129.63 A and c = 68.42 A. The asymmetric unit contains 1 subunit of beta-amylase, with a crystal volume per protein mass (VM) of 2.57 A3/Da and a solvent content of 52% by volume. The three-dimensional structure of the tetrameric beta-amylase from sweet potato has been determined by molecular replacement methods using the monomeric structure of soybean enzyme as the starting model. The refined subunit model contains 3,863 nonhydrogen protein atoms (488 amino acid residues) and 319 water oxygen atoms. The current R-value is 20.3% for data in the resolution range of 8-2.3 A (with 2 sigma cut-off) with good stereochemistry. The subunit structure of sweet potato beta-amylase (crystallized in the absence of alpha-cyclodextrin) is very similar to that of soybean beta-amylase (complexed with alpha-cyclodextrin). The root-mean-square (RMS) difference for 487 equivalent C alpha atoms of the two beta-amylases is 0.96 A. Each subunit of sweet potato beta-amylase is composed of a large (alpha/beta)8 core domain, a small one made up of three long loops [L3 (residues 91-150), L4 (residues 183-258), and L5 (residues 300-327)], and a long C-terminal loop formed by residues 445-493. Conserved Glu 187, believed to play an important role in catalysis, is located at the cleft between the (alpha/beta)8 barrel core and a small domain made up of three long loops (L3, L4, and L5). Conserved Cys 96, important in the inactivation of enzyme activity by sulfhydryl reagents, is located at the entrance of the (alpha/beta)8 barrel.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21085740

M.Rejzek, C.E.Stevenson, A.M.Southard, D.Stanley, K.Denyer, A.M.Smith, M.J.Naldrett, D.M.Lawson, and R.A.Field (2011).
Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley β-amylase.

Mol Biosyst, 7, 718-730.

PDB codes:

2xff 2xfr 2xfy 2xg9 2xgb 2xgi

12641711

A.Díaz, C.Sieiro, and T.G.Villa (2003).
Production and partial characterization of a beta-amylase by Xanthophyllomyces dendrorhous.

Lett Appl Microbiol, 36, 203-207.

11733023

E.J.Van Damme, J.Hu, A.Barre, B.Hause, G.Baggerman, P.Rougé, and W.J.Peumans (2001).
Purification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes.

Eur J Biochem, 268, 6263-6273.

10089328

T.Yamane, H.Tasaki, F.Matsumoto, A.Suzuki, N.Uozumi, and T.Ashida (1999).
Crystallization and preliminary x-ray analysis of beta-amylase from Bacillus polymyxa.

Acta Crystallogr D Biol Crystallogr, 55, 898-900.

9677422

M.Adachi, B.Mikami, T.Katsube, and S.Utsumi (1998).
Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.

J Biol Chem, 273, 19859-19865.

PDB code:

1bfn

9761914

M.J.Cho, S.S.Cha, J.H.Park, H.J.Cha, H.S.Lee, K.H.Park, and B.H.Oh (1998).
Preliminary X-ray crystallographic analysis of a novel maltogenic amylase from Bacillus stearothermophilus ET1.

Acta Crystallogr D Biol Crystallogr, 54, 416-418.

8535789

C.Wiesmann, G.Beste, W.Hengstenberg, and G.E.Schulz (1995).
The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.

Structure, 3, 961-968.

PDB code:

1pbg

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.