3VU2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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This is version 2.0 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

  • DOI: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplasticA, B702Oryza sativa Japonica GroupMutation(s): 1 
Gene Names: SBE1RBE1Os06g0726400LOC_Os06g51084P0017G10.8-1P0017G10.8-2P0548E04.28-1P0548E04.28-2
EC: 2.4.1.18
UniProt
Find proteins for Q01401 (Oryza sativa subsp. japonica)
Explore Q01401 
Go to UniProtKB:  Q01401
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01401
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC, D 5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G50146AM
GlyCosmos:  G50146AM
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900030
Query on PRD_900030
C, Dalpha-maltopentaoseOligosaccharide / Substrate analog Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.81α = 90
b = 66.56β = 89.97
c = 169.625γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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