6BGC | pdb_00006bgc

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.220 (Depositor), 0.221 (DCC)
R-Value Work:
0.180 (Depositor), 0.184 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.3373
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.220 (Depositor), 0.221 (DCC)
R-Value Work: 0.180 (Depositor), 0.184 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-01-31

Deposition Author(s):

Brautigam, C.A.

Norgard, M.V.

Deka, R.K.

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

Revision History (Full details and data files)

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