3GXO

Structure of the Mitomycin 7-O-methyltransferase MmcR with bound Mitomycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.255 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view detailsBest fitted MQAClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Structural characterization of the mitomycin 7-O-methyltransferase.

Singh, S.Chang, A.Goff, R.D.Bingman, C.A.Gruschow, S.Sherman, D.H.Phillips, G.N.Thorson, J.S.

(2011) Proteins 79: 2181-2188

  • DOI: https://doi.org/10.1002/prot.23040
  • Primary Citation of Related Structures:  
    3GWZ, 3GXO

  • PubMed Abstract: 

    Mitomycins are quinone-containing antibiotics, widely used as antitumor drugs in chemotherapy. Mitomycin-7-O-methyltransferase (MmcR), a key tailoring enzyme involved in the biosynthesis of mitomycin in Streptomyces lavendulae, catalyzes the 7-O-methylation of both C9β- and C9α-configured 7-hydroxymitomycins. We have determined the crystal structures of the MmcR-S-adenosylhomocysteine (SAH) binary complex and MmcR-SAH-mitomycin A (MMA) ternary complex at resolutions of 1.9and 2.3 Å, respectively. The study revealed MmcR to adopt a common S-adenosyl-L-methionine-dependent O-methyltransferase fold and the presence of a structurally conserved active site general acid-base pair is consistent with a proton-assisted methyltransfer common to most methyltransferases. Given the importance of C7 alkylation to modulate mitomycin redox potential, this study may also present a template toward the future engineering of catalysts to generate uniquely bioactive mitomycins.


  • Organizational Affiliation

    Division of Pharmaceutical Sciences, Wisconsin Center for Natural Product Research, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MmcRA,
B [auth D],
C,
D [auth B]
369Streptomyces lavendulaeMutation(s): 0 
Gene Names: mmcR
EC: 2.1.1.316
UniProt
Find proteins for Q9X5T6 (Streptomyces lavendulae)
Explore Q9X5T6 
Go to UniProtKB:  Q9X5T6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X5T6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
G [auth D],
K [auth C],
M [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
MQA
Query on MQA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth D],
L [auth C],
N [auth B]
[(1aS,8S,8aR,8bS)-6,8a-dimethoxy-5-methyl-4,7-dioxo-1,1a,2,4,7,8,8a,8b-octahydroazireno[2',3':3,4]pyrrolo[1,2-a]indol-8-yl]methyl carbamate
C16 H19 N3 O6
HYFMSAFINFJTFH-NGSRAFSJSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth D],
J [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
B [auth D],
C,
D [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.841α = 90
b = 98.844β = 90
c = 171.045γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view detailsBest fitted MQAClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-22
    Changes: Data collection
  • Version 1.5: 2024-11-20
    Changes: Data collection, Structure summary