3U95

Crystal structure of a putative alpha-glucosidase from Thermotoga neapolitana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure and thermostability of a putative alpha-glucosidase from Thermotoga neapolitana

Yun, B.Y.Jun, S.Y.Kim, N.A.Yoon, B.Y.Piao, S.Park, S.H.Jeong, S.H.Lee, H.Ha, N.C.

(2011) Biochem Biophys Res Commun 416: 92-98

  • DOI: 10.1016/j.bbrc.2011.11.002
  • Primary Citation of Related Structures:  
    3U95

  • PubMed Abstract: 
  • Glycoside hydrolase family 4 (GH4) represents an unusual group of glucosidases with a requirement for NAD(+), Mn(2+), and reducing conditions. We found a putative α-glucosidase belonging to GH4 in hyperthermophilic Gram-negative bacterium Thermotoga ...

    Glycoside hydrolase family 4 (GH4) represents an unusual group of glucosidases with a requirement for NAD(+), Mn(2+), and reducing conditions. We found a putative α-glucosidase belonging to GH4 in hyperthermophilic Gram-negative bacterium Thermotoga neapolitana. In this study, we recombinantly expressed the putative α-glycosidase from T. neapolitana, and determined the crystal structure of the protein at a resolution of 2.0Å in the presence of Mn(2+) but in the absence of NAD(+). The structure showed the dimeric assembly and the Mn(2+) coordination that other GH4 enzymes share. In comparison, we observed structural changes in T. neapolitana α-glucosidase by the binding of NAD(+), which also increased the thermostability. Numerous arginine-mediated salt-bridges were observed in the structure, and we confirmed that the salt bridges correlated with the thermostability of the proteins. Disruption of the salt bridge that linked N-terminal and C-terminal parts at the surface dramatically decreased the thermostability. A mutation that changed the internal salt bridge to a hydrogen bond also decreased the thermostability of the protein. This study will help us to understand the function of the putative glucosidase and the structural features that affect the thermostability of the protein.


    Organizational Affiliation

    Department of Manufacturing Pharmacy, College of Pharmacy and Research Institute for Drug Development, Pusan National University, Geumjeong-gu, Busan 609-735, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoside hydrolase, family 4A, B, C, D, E, F477Thermotoga neapolitana DSM 4359Mutation(s): 0 
Gene Names: CTN_1830
Find proteins for B9KAM3 (Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NS-E))
Explore B9KAM3 
Go to UniProtKB:  B9KAM3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A, B, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.532α = 90
b = 154.532β = 90
c = 139.065γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-26
    Type: Initial release