Crystal structure of a putative alpha-glucosidase from Thermotoga neapolitana

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

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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: https://doi.org/10.1016/j.bbrc.2011.11.002
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase, family 4
A, B, C, D, E
A, B, C, D, E, F
477Thermotoga neapolitana DSM 4359Mutation(s): 0 
Gene Names: CTN_1830
Find proteins for B9KAM3 (Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NBRC 107923 / NS-E))
Explore B9KAM3 
Go to UniProtKB:  B9KAM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9KAM3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations