4JMD

Enduracididine biosynthesis enzyme MppR complexed with the condensation product of pyruvate and imidazole 4-carboxaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of MppR, an Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus: Functional Diversity in the Acetoacetate Decarboxylase-like Superfamily.

Burroughs, A.M.Hoppe, R.W.Goebel, N.C.Sayyed, B.H.Voegtline, T.J.Schwabacher, A.W.Zabriskie, T.M.Silvaggi, N.R.

(2013) Biochemistry 52: 4492-4506

  • DOI: 10.1021/bi400397k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nonproteinogenic amino acid enduracididine is a critical component of the mannopeptimycins, cyclic glycopeptide antibiotics with activity against drug-resistant pathogens, including methicillin-resistant Staphylococcus aureus. Enduracididine is p ...

    The nonproteinogenic amino acid enduracididine is a critical component of the mannopeptimycins, cyclic glycopeptide antibiotics with activity against drug-resistant pathogens, including methicillin-resistant Staphylococcus aureus. Enduracididine is produced in Streptomyces hygroscopicus by three enzymes, MppP, MppQ, and MppR. On the basis of primary sequence analysis, MppP and MppQ are pyridoxal 5'-phosphate-dependent aminotransferases; MppR shares a low, but significant, level of sequence identity with acetoacetate decarboxylase. The exact reactions catalyzed by each enzyme and the intermediates involved in the route to enduracididine are currently unknown. Herein, we present biochemical and structural characterization of MppR that demonstrates a catalytic activity for this enzyme and provides clues about its role in enduracididine biosynthesis. Bioinformatic analysis shows that MppR belongs to a previously uncharacterized family within the acetoacetate decarboxylase-like superfamily (ADCSF) and suggests that MppR-like enzymes may catalyze reactions diverging from the well-characterized, prototypical ADCSF decarboxylase activity. MppR shares a high degree of structural similarity with acetoacetate decarboxylase, though the respective quaternary structures differ markedly and structural differences in the active site explain the observed loss of decarboxylase activity. The crystal structure of MppR in the presence of a mixture of pyruvate and 4-imidazolecarboxaldehyde shows that MppR catalyzes the aldol condensation of these compounds and subsequent dehydration. Surprisingly, the structure of MppR in the presence of "4-hydroxy-2-ketoarginine" shows the correct 4R enantiomer of "2-ketoenduracididine" bound to the enzyme. These data, together with bioinformatic analysis of MppR homologues, identify a novel family within the acetoacetate decarboxylase-like superfamily with divergent active site structure and, consequently, biochemical function.


    Organizational Affiliation

    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein mppR
A, B
302Streptomyces hygroscopicusMutation(s): 0 
Gene Names: mppR
Find proteins for Q643B8 (Streptomyces hygroscopicus)
Go to UniProtKB:  Q643B8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4IC
Query on 4IC

Download SDF File 
Download CCD File 
A, B
(3E)-4-(1H-imidazol-4-yl)but-3-enoic acid
C7 H8 N2 O2
KGQDUHSSIRUHKI-OWOJBTEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.147 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.000α = 90.00
b = 110.000β = 90.00
c = 87.800γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-13 
  • Released Date: 2013-07-03 
  • Deposition Author(s): Silvaggi, N.R.

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description