8RVC | pdb_00008rvc

Crystal structure of alpha keto acid C-methyl-transferases MrsA bound to ketoarginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.220 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structures and Protein Engineering of the alpha-Keto Acid C-Methyltransferases SgvM and MrsA for Rational Substrate Transfer.

Sommer-Kamann, C.Breiltgens, J.Zou, Z.Gerhardt, S.Saleem-Batcha, R.Kemper, F.Einsle, O.Andexer, J.N.Muller, M.

(2024) Chembiochem 25: e202400258-e202400258

  • DOI: https://doi.org/10.1002/cbic.202400258
  • Primary Citation Related Structures: 
    8R4Z, 8RPR, 8RVC, 8RVS, 8RWM, 8RWW, 8RXF, 8RXG

  • PubMed Abstract: 

    S‑adenosyl-l-methionine-dependent methyltransferases (MTs) are involved in the C-methylation of a variety of natural products. The MTs SgvM from Streptomyces griseoviridis and MrsA from Pseudomonas syringae pv. syringae catalyze the methylation of the β-carbon atom of α-keto acids in the biosynthesis of the antibiotic natural products viridogrisein and 3‑methylarginine, respectively. MrsA shows high substrate selectivity for 5‑guanidino-2-oxovalerate, while other α-keto acids, such as the SgvM substrates 4-methyl-2-oxovalerate, 2-oxovalerate, and phenylpyruvate, are not accepted. Here we report the crystal structures of SgvM and MrsA in the apo form bound with substrate or S‑adenosyl-l-methionine. By investigating key residues for substrate recognition in the active sites of both enzymes and engineering MrsA by site-directed mutagenesis, the substrate range of MrsA was extended to accept α‑keto acid substrates of SgvM with uncharged and lipophilic β‑residues. Our results showcase the transfer of the substrate scope of α-keto acid MTs from different biosynthetic pathways by rational design.


  • Organizational Affiliation
    • University of Freiburg, Institute of pharmaceutical science, GERMANY.

Macromolecule Content 

  • Total Structure Weight: 83.19 kDa 
  • Atom Count: 5,784 
  • Modeled Residue Count: 680 
  • Deposited Residue Count: 740 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-ketoarginine methyltransferase
A, B
370Pseudomonas syringaeMutation(s): 0 
Gene Names: mrsA
EC: 2.1.1.243
UniProt
Find proteins for D5FKJ3 (Pseudomonas syringae pv. syringae)
Explore D5FKJ3 
Go to UniProtKB:  D5FKJ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5FKJ3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NWG
(Subject of Investigation/LOI)

Query on NWG



Download:Ideal Coordinates CCD File
C [auth A],
R [auth B]
5-[(diaminomethylidene)amino]-2-oxopentanoic acid
C6 H11 N3 O3
ARBHXJXXVVHMET-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A],
M [auth B],
N [auth B],
O [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
K [auth A],
L [auth B],
T [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
S [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.220 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.45α = 90
b = 65.873β = 90
c = 75.041γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata 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: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Database references, Structure summary