5AXG | pdb_00005axg

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus

• PDB DOI: https://doi.org/10.2210/pdb5AXG/pdb

• Classification: HYDROLASE
• Organism(s): Thermoanaerobacter pseudethanolicus ATCC 33223
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-29 Released: 2015-11-11 
• Deposition Author(s): Suzuki, N., Kishine, N., Fujimoto, Z., Sakurai, M., Momma, M., Ko, J.A., Nam, S.H., Kimura, A., Kim, Y.M.
• Funding Organization(s): Ministry of Agriculture, Forestry and Fisheries, National Research Foundation of Korea

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus

Suzuki, N., Kishine, N., Fujimoto, Z., Sakurai, M., Momma, M., Ko, J.A., Nam, S.H., Kimura, A., Kim, Y.M.

(2016) J Biochem 159: 331-339

• PubMed: 26494689 
• DOI: https://doi.org/10.1093/jb/mvv104
• Primary Citation Related Structures: 
  5AXG, 5AXH


• PubMed Abstract: 
  

  The crystal structures of the wild type and catalytic mutant Asp-312→Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (β/α)8-barrel and two β-domains located at both N- and C-terminal ends. The isomaltohexaose-complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (-4 to +2) in the catalytic cleft. Marked movement of the Trp-376 side-chain along with loop 6, which was the side wall component of the cleft at subsite +1, was observed to occupy subsite +1, indicating that it might expel the cleaved aglycone subsite after the hydrolysis reaction. Structural comparison with other mesophilic enzymes indicated that several structural features of TpDex, loop deletion, salt bridge and surface-exposed charged residue, may contribute to thermostability.

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Organizational Affiliation: 
• Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan; [e-mail] [e-mail].
Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan; [e-mail].
Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan;
Eco-Friendly Bio-material Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 580-185, Korea;
Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju 500-757, Korea;
Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nisi-9, Kita-ku, Sapporo 060-8589, Japan;
Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju 500-757, Korea; Bioenergy Research Center, Chonnam National University, Gwangju 500-757, Korea [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 144.35 kDa 
• Atom Count: 10,614 
• Modeled Residue Count: 1,167 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dextranase	A, B	618	Thermoanaerobacter pseudethanolicus ATCC 33223	Mutation(s): 0  Gene Names: Teth39_0264 EC: 3.2.1.11
UniProt
Find proteins for B0KBZ7 (Thermoanaerobacter pseudethanolicus (strain ATCC 33223 / 39E)) Explore B0KBZ7  Go to UniProtKB:  B0KBZ7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	M [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
PO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.342	α = 90
b = 98.992	β = 90
c = 171.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Suzuki, N., Kishine, N., Fujimoto, Z., Sakurai, M., Momma, M., Ko, J.A., Nam, S.H., Kimura, A., Kim, Y.M.

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Funding Organization	Location	Grant Number
Ministry of Agriculture, Forestry and Fisheries	Japan	25001A
National Research Foundation of Korea	Korea, Republic Of	2010-0020141

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description