Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.39 kDa 
• Atom Count: 6,781 
• Modelled Residue Count: 693 
• Deposited Residue Count: 755 
• Unique protein chains: 1

 3AML

Structure of the Starch Branching Enzyme I (BEI) from Oryza sativa L

• PDB DOI: 10.2210/pdb3AML/pdb

• Classification: TRANSFERASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-20 Released: 2011-09-28 
• Deposition Author(s): Kakuta, Y., Chaen, K., Noguchi, J., Vu, N., Kimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 

Literature

Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.

Noguchi, J., Chaen, K., Vu, N.T., Akasaka, T., Shimada, H., Nakashima, T., Nishi, A., Satoh, H., Omori, T., Kakuta, Y., Kimura, M.

(2011) Glycobiology 21: 1108-1116

• PubMed: 21493662 
• DOI: 10.1093/glycob/cwr049
• Primary Citation of Related Structures:  
  3AMK, 3AML


• PubMed Abstract: 
  

Starch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase.

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Organizational Affiliation: 

Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Os06g0726400 protein	A	755	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: Os06g0726400, SBE1, RBE1, LOC_Os06g51084, P0017G10.8-1, P0017G10.8-2, P0548E04.28-1, P0548E04.28-2 EC: 2.4.1.18
UniProt
Find proteins for Q01401 (Oryza sativa subsp. japonica) Explore Q01401  Go to UniProtKB:  Q01401

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SIN	IA [auth A], L [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
GOL	AA [auth A], BA [auth A], C [auth A], CA [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], GA [auth A], H [auth A], HA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	B [auth A], I [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.066	α = 90
b = 124.85	β = 97.29
c = 67.88	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Kakuta, Y., Chaen, K., Noguchi, J., Vu, N., Kimura, M.

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release