5XV5

Crystal structure of Rib7 mutant S88E from Methanosarcina mazei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Evolution of archaeal Rib7 and eubacterial RibG reductases in riboflavin biosynthesis: Substrate specificity and cofactor preference.

Chen, S.C.Yen, T.M.Chang, T.H.Liaw, S.H.

(2018) Biochem Biophys Res Commun 503: 195-201

  • DOI: 10.1016/j.bbrc.2018.06.002
  • Primary Citation of Related Structures:  
    5XV0, 5XV2, 5XV5, 5XUX

  • PubMed Abstract: 
  • Archaeal/fungal Rib7 and eubacterial RibG possess a reductase domain for ribosyl reduction in the second and third steps, respectively, of riboflavin biosynthesis. These enzymes are specific for an amino and a carbonyl group of the pyrimidine ring, respectively ...

    Archaeal/fungal Rib7 and eubacterial RibG possess a reductase domain for ribosyl reduction in the second and third steps, respectively, of riboflavin biosynthesis. These enzymes are specific for an amino and a carbonyl group of the pyrimidine ring, respectively. Here, several crystal structures of Methanosarcina mazei Rib7 are reported at 2.27-1.95 Å resolution, which are the first archaeal dimeric Rib7 structures. Mutational analysis displayed that no detectable activity was observed for the Bacillus subtilis RibG K151A, K151D, and K151E mutants, and the M. mazei Rib7 D33N, D33K, and E156Q variants, while 0.1-0.6% of the activity was detected for the M. mazei Rib7 N9A, S29A, D33A, and D57N variants. Our results suggest that Lys151 in B. subtilis RibG, while Asp33 together with Arg36 in M. mazei Rib7, ensure the specific substrate recognition. Unexpectedly, an endogenous NADPH cofactor is observed in M. mazei Rib7, in which the 2'-phosphate group interacts with Ser88, and Arg91. Replacement of Ser88 with glutamate eliminates the endogenous NADPH binding and switches preference to NADH. The lower melting temperature of ∼10 °C for the S88E and R91A mutants suggests that nature had evolved a tightly bound NADPH to greatly enhance the structural stability of archaeal Rib7.


    Organizational Affiliation

    Structural Biology Program, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei, 11221, Taiwan; Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei, 11221, Taiwan; Department of Medical Research and Education, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Road, Beitou District, Taipei, 11217, Taiwan. Electronic address: shliaw@ym.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved proteinA, B, C, D, E, F240Methanosarcina mazei Go1Mutation(s): 1 
Gene Names: MM_0826
EC: 1.1.1.302
UniProt
Find proteins for Q8PYN5 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PYN5 
Go to UniProtKB:  Q8PYN5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.16α = 90
b = 116.16β = 90
c = 380.801γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references