8DHD | pdb_00008dhd

Neutron crystal structure of maltotetraose bound tmMBP

• PDB DOI: https://doi.org/10.2210/pdb8DHD/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2022-06-27 Released: 2022-10-12 
• Deposition Author(s): Cuneo, M.J., Shukla, S., Myles, D.A.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

---

• Method: NEUTRON DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.272 (Depositor) 
• R-Value Work: 
  0.245 (Depositor) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography.

Shukla, S., Myles, D.A., Cuneo, M.J.

(2022) Sci Rep 12: 17647-17647

• PubMed: 36271099 
• DOI: https://doi.org/10.1038/s41598-022-20542-8
• Primary Citation Related Structures: 
  8DHD


• PubMed Abstract: 
  

  Numerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.

---

Organizational Affiliation: 
• Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
UT-ORNL Graduate School in Genome Science and Technology, The University of Tennessee at Knoxville, Knoxville, TN, 37966, USA.
Department of Microbiology and Immunology, Northwestern University, Chicago, IL, 60611, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. [e-mail].
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. [e-mail].
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. [e-mail].

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: SAXS

Macromolecule Content 

• Total Structure Weight: 42.73 kDa 
• Atom Count: 3,119 
• Modeled Residue Count: 378 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
maltose-binding protein MalE2	A	383	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_1839
UniProt
Find proteins for Q9S5Y1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9S5Y1  Go to UniProtKB:  Q9S5Y1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan: G87171PZ GlyCosmos: G87171PZ GlyGen: G87171PZ

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010	B	alpha-maltotetraose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.272 (Depositor) 
• R-Value Work:  0.245 (Depositor) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.915	α = 90
b = 56.34	β = 94.25
c = 90.001	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
LAUENORM	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Cuneo, M.J., Shukla, S., Myles, D.A.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2022-11-02
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description