2BHY | pdb_00002bhy

Crystal structure of Deinococcus radiodurans maltooligosyltrehalose trehalohydrolase in complex with trehalose

• PDB DOI: https://doi.org/10.2210/pdb2BHY/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-20 Released: 2005-03-31 
• Deposition Author(s): Timmins, J., Leiros, H.-K.S., Leonard, G., Leiros, I., McSweeney, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.152 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.128 (Depositor) 
• R-Value Observed: 
  0.129 (Depositor) 

Literature

Crystal Structure of Maltooligosyltrehalose Trehalohydrolase from Deinococcus Radiodurans in Complex with Disaccharides

Timmins, J., Leiros, H.-K.S., Leonard, G., Leiros, I., Mcsweeney, S.

(2005) J Mol Biology 347: 949

• PubMed: 15784255 
• DOI: https://doi.org/10.1016/j.jmb.2005.02.011
• Primary Citation Related Structures: 
  2BHU, 2BHY, 2BHZ


• PubMed Abstract: 
  

  Trehalose (alpha-D-glucopyranosyl-1,1-alpha-D-glucopyranose) is a non-reducing diglucoside found in various organisms that serves as a carbohydrate reserve and as an agent that protects against a variety of physical and chemical stresses. Deinococcus radiodurans possesses an alternative biosynthesis pathway for the synthesis of trehalose from maltooligosaccharides. This reaction is mediated by two enzymes: maltooligosyltrehalose synthase (MTSase) and maltooligosyltrehalose trehalohydrolase (MTHase). Here, we present the 1.1A resolution crystal structure of MTHase. It consists of three major domains: two beta-sheet domains and a conserved glycosidase (beta/alpha)8 barrel catalytic domain. Three subdomains consisting of short insertions were identified within the catalytic domain. Subsequently, structures of MTHase in complex with maltose and trehalose were obtained at 1.2 A and 1.5 A resolution, respectively. These structures reveal the importance of the three inserted subdomains in providing the key residues required for substrate recognition. Trehalose is recognised specifically in the +1 and +2 binding subsites by an extensive hydrogen-bonding network and a strong hydrophobic stacking interaction in between two aromatic residues. Moreover, upon binding to maltose, which mimics the substrate sugar chain, a major concerted conformational change traps the sugar chain in the active site. The presence of magnesium in the active site of the MTHase-maltose complex suggests that MTHase activity may be regulated by divalent cations.

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Organizational Affiliation: 
• Macromolecular Crystallography Group, European Synchrotron Radiation Facility, B.P. 220, 6 rue Jules Horowitz, F-38043 Grenoble Cedex, France.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 70.73 kDa 
• Atom Count: 6,219 
• Modeled Residue Count: 580 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MALTOOLIGOSYLTREHALOSE TREHALOHYDROLASE	A	602	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  EC: 3.2.1.1 (PDB Primary Data), 3.2.1.141 (UniProt)
UniProt
Find proteins for Q9RX51 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RX51  Go to UniProtKB:  Q9RX51

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B, C, D, E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	L [auth A], M [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
TRS	I [auth A], J [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
BME	K [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
MG	N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	B, C, D, E, F, G, H	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.152 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.128 (Depositor) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.029	α = 90
b = 66.556	β = 90
c = 153.141	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-31 
Deposition Author(s): Timmins, J., Leiros, H.-K.S., Leonard, G., Leiros, I., McSweeney, S.

Revision History  

• Version 1.0: 2005-03-31
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2025-04-09
  Changes: Advisory, Data collection, Database references, Structure summary
• Version 3.0: 2025-10-01
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary