5B7N

Crystal structure of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.399 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Analyses of Periplasmic 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase from Aeromonas hydrophila.

Xu, Y.Wang, L.Chen, J.Zhao, J.Fan, S.Dong, Y.Ha, N.C.Quan, C.

(2017) Biochemistry 56: 5347-5355

  • DOI: 10.1021/acs.biochem.7b00691
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Gram-negative, rod-shaped bacterium Aeromonas hydrophila has two multifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzymes, MtaN-1 and MtaN-2, that differ from those in other bacteria. These proteins are essential ...

    The Gram-negative, rod-shaped bacterium Aeromonas hydrophila has two multifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzymes, MtaN-1 and MtaN-2, that differ from those in other bacteria. These proteins are essential for several metabolic pathways, including biological methylation, polyamine biosynthesis, methionine recycling, and bacterial quorum sensing. To gain insight into how these two proteins function, we determined four high-resolution crystal structures of MtaN-1 in its apo form and in complex with the substrates S-adenosyl-l-homocysteine, 5'-methylthioadenosine, and 5'-deoxyadenosine. We found that the domain structures were generally similar, although slight differences were evident. The crystal structure demonstrates that AhMtaN-1 has an extension of the binding pocket and revealed that a tryptophan in the active site (Trp199) may play a major role in substrate binding, unlike in other MTAN proteins. Mutation of the Trp199 residue completely abolished the enzyme activity. Trp199 was identified as an active site residue that is essential for catalysis. Furthermore, biochemical characterization of AhMtaN-1 and AhMtaN-2 demonstrated that AhMtaN-1 exhibits inherent trypsin resistance that is higher than that of AhMtaN-2. Additionally, the thermally unfolded AhMtaN-2 protein is capable of refolding into active forms, whereas the thermally unfolded AhMtaN-1 protein does not have this ability. Examining the different biochemical characteristics related to the functional roles of AhMtaN-1 and AhMtaN-2 would be interesting. Indeed, the biochemical characterization of these structural features would provide a structural basis for the design of new antibiotics against A. hydrophila.


    Organizational Affiliation

    Department of Bioengineering, College of Life Science, Dalian Minzu University , Dalian 116600, Liaoning, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MTA/SAH nucleosidase
A, B
248Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)Mutation(s): 0 
Gene Names: mtnN-1
EC: 3.2.2.16, 3.2.2.9
Find proteins for A0KGU9 (Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240))
Go to UniProtKB:  A0KGU9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.399 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.085α = 90.00
b = 103.085β = 90.00
c = 118.923γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data processing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-06-08 
  • Released Date: 2016-12-21 
  • Deposition Author(s): Xu, Y.

Funding OrganizationLocationGrant Number
the National Natural Science Foundation of ChinaChina31200556
the Program for Liaoning Excellent Talents in UniversityChinaLJQ2015030
the Fundamental Research Funds for the Central UniversitiesChinaDC201502020203

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references