6BGC

The crystal structure of the W145A variant of TpMglB-2 (Tp0684) with bound glucose

• PDB DOI: https://doi.org/10.2210/pdb6BGC/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Treponema pallidum subsp. pallidum str. Nichols
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-27 Released: 2018-01-31 
• Deposition Author(s): Brautigam, C.A., Norgard, M.V., Deka, R.K.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of MglB-2 (TP0684), a topologically variant d-glucose-binding protein from Treponema pallidum, reveal a ligand-induced conformational change.

Brautigam, C.A., Deka, R.K., Liu, W.Z., Norgard, M.V.

(2018) Protein Sci 27: 880-885

• PubMed: 29318719 
• DOI: https://doi.org/10.1002/pro.3373
• Primary Citation of Related Structures:  
  6BGC, 6BGD


• PubMed Abstract: 
  

  Previously, we determined the crystal structure of apo-TpMglB-2, a d-glucose-binding component of a putative ABC transporter from the syphilis spirochete Treponema pallidum. The protein had an unusual topology for this class of proteins, raising the question of whether the d-glucose-binding mode would be different in TpMglB-2. Here, we present the crystal structures of a variant of TpMglB-2 with and without d-glucose bound. The structures demonstrate that, despite its aberrant topology, the protein undergoes conformational changes and binds d-glucose similarly to other Mgl-type proteins, likely facilitating d-glucose uptake in T. pallidum.

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Organizational Affiliation: 

Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.

Biological Assembly 1  

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

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

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 83.89 kDa 
• Atom Count: 5,777 
• Modelled Residue Count: 736 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose/galactose-binding lipoprotein	A, B	387	Treponema pallidum subsp. pallidum str. Nichols	Mutation(s): 1  Gene Names: mglB, tpp38, TP_0684
UniProt
Find proteins for Q08255 (Treponema pallidum (strain Nichols)) Explore Q08255  Go to UniProtKB:  Q08255

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC (Subject of Investigation/LOI)	C [auth A], F [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
EDO	E [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.257	α = 80.22
b = 61.592	β = 77.58
c = 70.35	γ = 72.72

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Brautigam, C.A., Norgard, M.V., Deka, R.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI056305

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Author supporting evidence
• Version 1.2: 2018-04-04
  Changes: Data collection, Database references
• Version 1.3: 2019-08-21
  Changes: Data collection, Database references
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary