6C5B | pdb_00006c5b

Crystal Structure Analysis of LaPhzM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.203 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Functional and Structural Analysis of Phenazine O-Methyltransferase LaPhzM from Lysobacter antibioticus OH13 and One-Pot Enzymatic Synthesis of the Antibiotic Myxin.

Jiang, J.Guiza Beltran, D.Schacht, A.Wright, S.Zhang, L.Du, L.

(2018) ACS Chem Biol 13: 1003-1012

  • DOI: https://doi.org/10.1021/acschembio.8b00062
  • Primary Citation Related Structures: 
    6C5B

  • PubMed Abstract: 

    Myxin is a well-known antibiotic that had been used for decades. It belongs to the phenazine natural products that exhibit various biological activities, which are often dictated by the decorating groups on the heteroaromatic three-ring system. The three rings of myxin carry a number of decorations, including an unusual aromatic N5, N10-dioxide. We previously showed that phenazine 1,6-dicarboxylic acid (PDC) is the direct precursor of myxin, and two redox enzymes (LaPhzS and LaPhzNO1) catalyze the decarboxylative hydroxylation and aromatic N-oxidations of PDC to produce iodinin (1.6-dihydroxy- N5, N10-dioxide phenazine). In this work, we identified the LaPhzM gene from Lysobacter antibioticus OH13 and demonstrated that LaPhzM encodes a SAM-dependent O-methyltransferase converting iodinin to myxin. The results further showed that LaPhzM is responsible for both monomethoxy and dimethoxy formation in all phenazine compounds isolated from strain OH13. LaPhzM exhibits relaxed substrate selectivity, catalyzing O-methylation of phenazines with non-, mono-, or di- N-oxide. In addition, we demonstrated a one-pot biosynthesis of myxin by in vitro reconstitution of the three phenazine-ring decorating enzymes. Finally, we determined the X-ray crystal structure of LaPhzM with a bound cofactor at 1.4 Å resolution. The structure provided molecular insights into the activity and selectivity of the first characterized phenazine O-methyltransferase. These results will facilitate future exploitation of the thousands of phenazines as new antibiotics through metabolic engineering and chemoenzymatic syntheses.


  • Organizational Affiliation
    • Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.

Macromolecule Content 

  • Total Structure Weight: 75.38 kDa 
  • Atom Count: 5,732 
  • Modeled Residue Count: 664 
  • Deposited Residue Count: 682 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methyltransferase
A, B
341Lysobacter antibioticusMutation(s): 0 
EC: 2.1.1
UniProt
Find proteins for A0A172J1V3 (Lysobacter antibioticus)
Explore A0A172J1V3 
Go to UniProtKB:  A0A172J1V3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A172J1V3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH

Query on SAH



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
P33

Query on P33



Download:Ideal Coordinates CCD File
I [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
K [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.203 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.275α = 90
b = 81.017β = 98.23
c = 72.164γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 2.0: 2023-10-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary