4WVC

Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with Tris and D-glycerate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and substrate-binding mode of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8.

Miyazaki, T.Ichikawa, M.Iino, H.Nishikawa, A.Tonozuka, T.

(2015) J.Struct.Biol. 190: 21-30

  • DOI: 10.1016/j.jsb.2015.02.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycoside hydrolase family 63 (GH63) proteins are found in eukaryotes such as processing α-glucosidase I and also many bacteria and archaea. Recent studies have identified two bacterial and one plant GH63 mannosylglycerate hydrolases that act on both ...

    Glycoside hydrolase family 63 (GH63) proteins are found in eukaryotes such as processing α-glucosidase I and also many bacteria and archaea. Recent studies have identified two bacterial and one plant GH63 mannosylglycerate hydrolases that act on both glucosylglycerate and mannosylglycerate, which are compatible solutes found in many thermophilic prokaryotes and some plants. Here we report the 1.67-Å crystal structure of one of these GH63 mannosylglycerate hydrolases, Tt8MGH from Thermus thermophilus HB8, which is 99% homologous to mannosylglycerate hydrolase from T. thermophilus HB27. Tt8MGH consists of a single (α/α)6-barrel catalytic domain with two additional helices and two long loops which form a homotrimer. The structures of this protein in complexes with glucose or glycerate were also determined at 1.77- or 2.10-Å resolution, respectively. A comparison of these structures revealed that the conformations of three flexible loops were largely different from each other. The conformational changes may be induced by ligand binding and serve to form finger-like structures for holding substrates. These findings represent the first-ever proposed substrate recognition mechanism for GH63 mannosylglycerate hydrolase.


    Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B
420Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Find proteins for Q5SJN0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJN0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DGY
Query on DGY

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Download CCD File 
A, B
(2R)-2,3-DIHYDROXYPROPANOIC ACID
C3 H6 O4
RBNPOMFGQQGHHO-UWTATZPHSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.245 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.940α = 90.00
b = 92.940β = 90.00
c = 190.401γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
MOSFLMdata processing
SCALEPACKdata reduction
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references