3VU2 | pdb_00003vu2

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

PDB DOI: https://doi.org/10.2210/pdb3VU2/pdb

Classification: TRANSFERASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-06-14 Released: 2013-05-08
Deposition Author(s): Chaen, K., Kakuta, Y., Kimura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.286 (Depositor), 0.280 (DCC)
R-Value Work:
0.226 (Depositor), 0.220 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of the rice branching enzyme I (BEI) in complex with maltopentaose.

Chaen, K., Noguchi, J., Omori, T., Kakuta, Y., Kimura, M.

(2012) Biochem Biophys Res Commun 424: 508-511

PubMed: 22771800 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2012.06.145
Primary Citation of Related Structures:
3VU2

PubMed Abstract:
Starch branching enzyme (SBE) 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. We determined the crystal structure of the rice branching enzyme I (BEI) in complex with maltopentaose at a resolution of 2.2Å. Maltopentaose bound to a hydrophobic pocket formed by the N-terminal helix, carbohydrate-binding module 48 (CBM48), and α-amylase domain. In addition, glucose moieties could be observed at molecular surfaces on the N-terminal helix (α2) and CBM48. Amino acid residues involved in the carbohydrate bindings are highly conserved in other SBEs, suggesting their generally conserved role in substrate binding for SBEs.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 165.24 kDa
Atom Count: 12,313
Modeled Residue Count: 1,383
Deposited Residue Count: 1,404
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic	A, B	702	Oryza sativa Japonica Group	Mutation(s): 1 Gene Names: SBE1, RBE1, Os06g0726400, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01401
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	5		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G50146AM GlyCosmos: G50146AM

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	E [auth A], F [auth A], H [auth B], I [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900030 Query on PRD_900030	C, D	alpha-maltopentaose	Oligosaccharide / Substrate analog		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.286 (Depositor), 0.280 (DCC)
R-Value Work: 0.226 (Depositor), 0.220 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.81	α = 90
b = 66.56	β = 89.97
c = 169.625	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-08

Deposition Author(s):

Chaen, K.

Kakuta, Y.

Kimura, M.

Revision History (Full details and data files)

Version 1.0: 2013-05-08
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-03-20
Changes: Data collection, Database references, Structure summary