8TN2

Structure of S. hygroscopicus aminotransferase MppQ complexed with pyridoxal-5'-phosphate (PLP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

Starting Model: experimental
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Literature

Structural and Biochemical Characterization of MppQ, an L-Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus.

Vuksanovic, N.Melkonian, T.R.Serrano, D.A.Schwabacher, A.W.Silvaggi, N.R.

(2023) Biochemistry 62: 3105-3115

  • DOI: https://doi.org/10.1021/acs.biochem.3c00428
  • Primary Citation of Related Structures:  
    8TN2, 8TN3

  • PubMed Abstract: 

    MppQ is an enzyme of unknown function from Streptomyces hygroscopicus (ShMppQ) that operates in the biosynthesis of the nonproteinogenic amino acid L-enduracididine (L-End). Since L-End is a component of several peptides showing activity against antibiotic-resistant pathogens, understanding its biosynthetic pathway could facilitate the development of chemoenzymatic routes to novel antibiotics. Herein, we report on the crystal structures of ShMppQ complexed with pyridoxal-5'-phosphate (PLP) and pyridoxamine-5'-phosphate (PMP). ShMppQ is similar to fold-type I PLP-dependent aminotransferases like aspartate aminotransferase. The tertiary structure of ShMppQ is composed of an N-terminal extension, a large domain, and a small domain. The active site is placed at the junction of the large and small domains and includes residues from both protomers of the homodimer. We also report the first functional characterization of MppQ, which we incubated with the enzymatically produced 2-ketoenduracidine and observed the conversion to L-End, establishing ShMppQ as the final enzyme in L-End biosynthesis. Additionally, we have observed that MppQ has a relatively high affinity for 2-keto-5-guanidinovaleric acid (i.e., 2-ketoarginine), a shunt product of MppP, indicating the potential role of MppQ in increasing the efficiency of L-End biosynthesis by converting 2-ketoarginine back to the starting material, l-arginine. A panel of potential amino-donor substrates was tested for the transamination activity against a saturating concentration of 2-ketoarginine in end-point assays. Most l-Arg was produced with l-ornithine as the donor substrate. Steady-state kinetic analysis of the transamination reaction with l-Orn and 2-ketoarginine shows that the kinetic constants are in line with those for the amino donor substrate of other fold-type I aminotransferases.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLP-dependent aminotransferase MppQ
A, B
415Streptomyces hygroscopicusMutation(s): 0 
Gene Names: mppQ
UniProt
Find proteins for Q643B9 (Streptomyces hygroscopicus)
Explore Q643B9 
Go to UniProtKB:  Q643B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ643B9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.73α = 90
b = 114.5β = 90
c = 133.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1903899

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release