3HJE

Crystal structure of sulfolobus tokodaii hypothetical maltooligosyl trehalose synthase

• PDB DOI: https://doi.org/10.2210/pdb3HJE/pdb

• Classification: TRANSFERASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-21 Released: 2010-04-14 
• Deposition Author(s): Cielo, C.B.C., Okazaki, S., Suzuki, A., Mizushima, T., Masui, R., Kuramitsu, S., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Structure of ST0929, a putative glycosyl transferase from Sulfolobus tokodaii

Cielo, C.B.C., Okazaki, S., Suzuki, A., Mizushima, T., Masui, R., Kuramitsu, S., Yamane, T.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 397-400

• PubMed: 20383007 
• DOI: https://doi.org/10.1107/S1744309110006354
• Primary Citation of Related Structures:  
  3HJE


• PubMed Abstract: 
  

  The Sulfolobus tokodaii protein ST0929 shares close structural homology with S. acidocaldarius maltooligosyl trehalose synthase (SaMTSase), suggesting that the two enzymes share a common enzymatic mechanism. MTSase is one of a pair of enzymes that catalyze trehalose biosynthesis. The relative geometries of the ST0929 and SaMTSase active sites were found to be essentially identical. ST0929 also includes the unique tyrosine cluster that encloses the reducing-end glucose subunit in Sulfolobus sp. MTSases. The current structure provides insight into the structural basis of the increase in the hydrolase side reaction that is observed for mutants in which a phenylalanine residue is replaced by a tyrosine residue in the subsite +1 tyrosine cluster of Sulfolobus sp.

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Organizational Affiliation: 

Department of Biotechnology, School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 84.1 kDa 
• Atom Count: 6,957 
• Modelled Residue Count: 704 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
704aa long hypothetical glycosyltransferase	A	704	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: ST0929 EC: 5.4.99.15
UniProt
Find proteins for Q973H2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q973H2  Go to UniProtKB:  Q973H2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.992	α = 90
b = 86.1	β = 95.43
c = 70.13	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Cielo, C.B.C., Okazaki, S., Suzuki, A., Mizushima, T., Masui, R., Kuramitsu, S., Yamane, T.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-02
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary