Catalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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Crystal structure of the catalytic domain of a GH16 beta-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94

Takagi, E.Hatada, Y.Akita, M.Ohta, Y.Yokoi, G.Miyazaki, T.Nishikawa, A.Tonozuka, T.

(2015) Biosci Biotechnol Biochem 79: 625-632

  • DOI: https://doi.org/10.1080/09168451.2014.988680
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94, has a β-agarase (MtAgaA) belonging to the glycoside hydrolase family (GH) 16. The optimal temperature of this bacterium for growth is 43-49 °C, and MtAgaA is stable at 60 °C, which is one of the most thermostable enzymes among GH16 β-agarases. Here, we determined the catalytic domain structure of MtAgaA. MtAgaA consists of a β-jelly roll fold, as observed in other GH16 enzymes. The structure of MtAgaA was most similar to two β-agarases from Zobellia galactanivorans, ZgAgaA, and ZgAgaB. Although the catalytic cleft structure of MtAgaA was similar to ZgAgaA and ZgAgaB, residues at subsite -4 of MtAgaA were not conserved between them. Also, an α-helix, designated as α4', was uniquely located near the catalytic cleft of MtAgaA. A comparison of the structures of the three enzymes suggested that multiple factors, including increased numbers of arginine and proline residues, could contribute to the thermostability of MtAgaA.

  • Organizational Affiliation

    a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Agarase282Microbulbifer thermotoleransMutation(s): 0 
Gene Names: agaA
Find proteins for Q6F4N4 (Microbulbifer thermotolerans)
Explore Q6F4N4 
Go to UniProtKB:  Q6F4N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6F4N4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.624α = 90
b = 69.394β = 90
c = 90.367γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description