8BIG

O-Methyltransferase Plu4895 in complex with SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments.

Huber, E.M.Kreling, L.Heinrich, A.K.Dunnebacke, M.Pothig, A.Bode, H.B.Groll, M.

(2023) Structure 31: 573

  • DOI: https://doi.org/10.1016/j.str.2023.03.001
  • Primary Citation of Related Structures:  
    8BGT, 8BGX, 8BGY, 8BGZ, 8BH0, 8BIB, 8BIC, 8BID, 8BIE, 8BIF, 8BIG, 8BIH, 8BII, 8BIJ, 8BIR

  • PubMed Abstract: 

    Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdus luminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P. luminescens. Activity assays in vitro and deletion experiments in vivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found in vitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.


  • Organizational Affiliation

    Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany. Electronic address: eva.huber@tum.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
methyltransferase Plu4895
A, B, C, D, E
A, B, C, D, E, F, G, H
318Photorhabdus laumondii subsp. laumondii TTO1Mutation(s): 0 
UniProt
Find proteins for Q7MY04 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Explore Q7MY04 
Go to UniProtKB:  Q7MY04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MY04
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
M [auth C]
N [auth D]
S [auth E]
I [auth A],
L [auth B],
M [auth C],
N [auth D],
S [auth E],
U [auth F],
V [auth G],
Y [auth H]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
R [auth D],
X [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
J [auth A],
O [auth D],
P [auth D],
T [auth E]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A],
Q [auth D],
Z [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
W [auth G]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.06α = 90
b = 95.9β = 90
c = 522.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2023-05-17
    Changes: Database references
  • Version 1.3: 2023-11-15
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-02-07
    Changes: Refinement description