4M72

Mutant structure of methyltransferase from Streptomyces hygroscopicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report



Literature

Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase

Zou, X.W.Liu, Y.C.Hsu, N.S.Huang, C.J.Lyu, S.Y.Chan, H.C.Chang, C.Y.Yeh, H.W.Lin, K.H.Wu, C.J.Tsai, M.D.Li, T.L.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1549-1560

  • DOI: 10.1107/S1399004714005239
  • Primary Citation of Related Structures:  
    4M6X, 4M6Y, 4M71, 4M72, 4M73, 4M74, 4KIB, 4KIC, 4KIF, 4KIG

  • PubMed Abstract: 
  • In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a ...

    In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a building unit of the glycopeptide antibiotic mannopeptimycin. The gene product of mppJ from the mannopeptimycin-biosynthetic gene cluster is the MT that methylates the benzylic C atom of phenylpyruvate (Ppy) to give βMePpy. Although the benzylic C atom of Ppy is acidic, how its nucleophilicity is further enhanced to become an acceptor for C-methylation has not conclusively been determined. Here, a structural approach is used to address the mechanism of MppJ and to engineer it for new functions. The purified MppJ displays a turquoise colour, implying the presence of a metal ion. The crystal structures reveal MppJ to be the first ferric ion SAM-dependent MT. An additional four structures of binary and ternary complexes illustrate the molecular mechanism for the metal ion-dependent methyltransfer reaction. Overall, MppJ has a nonhaem iron centre that bind, orients and activates the α-ketoacid substrate and has developed a sandwiched bi-water device to avoid the formation of the unwanted reactive oxo-iron(IV) species during the C-methylation reaction. This discovery further prompted the conversion of the MT into a structurally/functionally unrelated new enzyme. Through stepwise mutagenesis and manipulation of coordination chemistry, MppJ was engineered to perform both Lewis acid-assisted hydration and/or O-methyltransfer reactions to give stereospecific new compounds. This process was validated by six crystal structures. The results reported in this study will facilitate the development and design of new biocatalysts for difficult-to-synthesize biochemicals.


    Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyltransferase MppJAB337Streptomyces hygroscopicusMutation(s): 2 
Gene Names: mppJ
EC: 2.1.1 (PDB Primary Data), 2.1.1.281 (UniProt)
Find proteins for Q643C8 (Streptomyces hygroscopicus)
Explore Q643C8 
Go to UniProtKB:  Q643C8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
M72
Query on M72

Download CCD File 
A, B
(2R,3R)-2-hydroxy-3-methoxy-3-phenylpropanoic acid
C10 H12 O4
GXFJZAOTDOMEEI-RKDXNWHRSA-N
 Ligand Interaction
HF2
Query on HF2

Download CCD File 
A, B
(2R)-2-hydroxy-3-phenylpropanoic acid
C9 H10 O3
VOXXWSYKYCBWHO-MRVPVSSYSA-N
 Ligand Interaction
FE
Query on FE

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A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.871α = 90
b = 97.136β = 90
c = 135.234γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release