7BVT | pdb_00007bvt

Crystal structure of cyclic alpha-maltosyl-1,6-maltose binding protein from Arthrobacter globiformis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.207 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.185 (Depositor) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Molecular analysis of cyclic alpha-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway.

Kohno, M.Arakawa, T.Sunagawa, N.Mori, T.Igarashi, K.Nishimoto, T.Fushinobu, S.

(2020) PLoS One 15: e0241912-e0241912

  • DOI: https://doi.org/10.1371/journal.pone.0241912
  • Primary Citation Related Structures: 
    7BVT

  • PubMed Abstract: 

    Cyclic α-maltosyl-(1→6)-maltose (CMM) is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. Here, we report functional and structural analyses on CMM-binding protein (CMMBP), which is a substrate-binding protein (SBP) of an ABC importer system of the bacteria Arthrobacter globiformis. Isothermal titration calorimetry analysis revealed that CMMBP specifically bound to CMM with a Kd value of 9.6 nM. The crystal structure of CMMBP was determined at a resolution of 1.47 Å, and a panose molecule was bound in a cleft between two domains. To delineate its structural features, the crystal structure of CMMBP was compared with other SBPs specific for carbohydrates, such as cyclic α-nigerosyl-(1→6)-nigerose and cyclodextrins. These results indicate that A. globiformis has a unique metabolic pathway specialized for CMM.


  • Organizational Affiliation
    • Department of Biotechnology, The University of Tokyo, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 45 kDa 
  • Atom Count: 3,370 
  • Modeled Residue Count: 391 
  • Deposited Residue Count: 416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical sugar ABC-transporter sugar binding protein416Arthrobacter globiformisMutation(s): 0 
Gene Names: cmmC
UniProt
Find proteins for D2YYD8 (Arthrobacter globiformis)
Explore D2YYD8 
Go to UniProtKB:  D2YYD8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2YYD8
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan: G05704WW
GlyCosmos: G05704WW
GlyGen: G05704WW

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.207 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.185 (Depositor) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.077α = 90
b = 92.077β = 90
c = 161.584γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan15H02443

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description