Skip to main content

 5IWS | pdb_00005iws

Crystal structure of the transporter MalT, the EIIC domain from the maltose-specific phosphotransferase system


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.282 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5IWS

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

Literature

The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport.

McCoy, J.G., Ren, Z., Stanevich, V., Lee, J., Mitra, S., Levin, E.J., Poget, S., Quick, M., Im, W., Zhou, M.

(2016) Structure 24: 956-964

  • DOI: https://doi.org/10.1016/j.str.2016.04.003
  • Primary Citation Related Structures: 
    5IWS

  • PubMed Abstract: 

    The phosphoenolpyruvate:carbohydrate phosphotransferase systems are found in bacteria, where they play central roles in sugar uptake and regulation of cellular uptake processes. Little is known about how the membrane-embedded components (EIICs) selectively mediate the passage of carbohydrates across the membrane. Here we report the functional characterization and 2.55-Å resolution structure of a maltose transporter, bcMalT, belonging to the glucose superfamily of EIIC transporters. bcMalT crystallized in an outward-facing occluded conformation, in contrast to the structure of another glucose superfamily EIIC, bcChbC, which crystallized in an inward-facing occluded conformation. The structures differ in the position of a structurally conserved substrate-binding domain that is suggested to play a central role in sugar transport. In addition, molecular dynamics simulations suggest a potential pathway for substrate entry from the periplasm into the bcMalT substrate-binding site. These results provide a mechanistic framework for understanding substrate recognition and translocation for the glucose superfamily EIIC transporters.


  • Organizational Affiliation: 
    • Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.

Macromolecule Content 

  • Total Structure Weight: 52.06 kDa 
  • Atom Count: 3,439 
  • Modeled Residue Count: 443 
  • Deposited Residue Count: 470 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)470Bacillus cereus E33LMutation(s): 0 
Gene Names: ptsG, BCE33L0344
EC: 2.7.1.69
Membrane Entity: Yes 
UniProt
Find proteins for Q63GK8 (Bacillus cereus (strain ZK / E33L))
Explore Q63GK8 
Go to UniProtKB:  Q63GK8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63GK8
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.282 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.633α = 90
b = 108.182β = 90
c = 139.329γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098878
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL086392
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK088057
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54GM095315
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54GM087519
American Heart AssociationUnited States12EIA8850017
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesR12MZ

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary