3PXS | pdb_00003pxs

Crystal Structure of Diferrous MauG in Complex with Pre-Methylamine Dehydrogenase:


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.229 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.177 (Depositor) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3PXS

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of CO and NO Adducts of MauG in Complex with Pre-Methylamine Dehydrogenase: Implications for the Mechanism of Dioxygen Activation.

Yukl, E.T.Goblirsch, B.R.Davidson, V.L.Wilmot, C.M.

(2011) Biochemistry 50: 2931-2938

  • DOI: https://doi.org/10.1021/bi200023n
  • Primary Citation Related Structures: 
    3PXS, 3PXT, 3PXW

  • PubMed Abstract: 

    MauG is a diheme enzyme responsible for the post-translational formation of the catalytic tryptophan tryptophylquinone (TTQ) cofactor in methylamine dehydrogenase (MADH). MauG can utilize hydrogen peroxide, or molecular oxygen and reducing equivalents, to complete this reaction via a catalytic bis-Fe(IV) intermediate. Crystal structures of diferrous, Fe(II)-CO, and Fe(II)-NO forms of MauG in complex with its preMADH substrate have been determined and compared to one another as well as to the structure of the resting diferric MauG-preMADH complex. CO and NO each bind exclusively to the 5-coordinate high-spin heme with no change in ligation of the 6-coordinate low-spin heme. These structures reveal likely roles for amino acid residues in the distal pocket of the high-spin heme in oxygen binding and activation. Glu113 is implicated in the protonation of heme-bound diatomic oxygen intermediates in promoting cleavage of the O-O bond. Pro107 is shown to change conformation on the binding of each ligand and may play a steric role in oxygen activation by positioning the distal oxygen near Glu113. Gln103 is in a position to provide a hydrogen bond to the Fe(IV)═O moiety that may account for the unusual stability of this species in MauG.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States.

Macromolecule Content 

  • Total Structure Weight: 200.53 kDa 
  • Atom Count: 14,569 
  • Modeled Residue Count: 1,711 
  • Deposited Residue Count: 1,792 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methylamine utilization protein MauG
A, B
373Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: mauGPden_4736
EC: 1
UniProt
Find proteins for Q51658 (Paracoccus denitrificans (strain Pd 1222))
Explore Q51658 
Go to UniProtKB:  Q51658
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51658
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Methylamine dehydrogenase light chain
C, E
137Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: mauA
EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
UniProt
Find proteins for P22619 (Paracoccus denitrificans)
Explore P22619 
Go to UniProtKB:  P22619
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22619
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Methylamine dehydrogenase heavy chain
D, F
386Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: mauB
EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
UniProt
Find proteins for A1BB97 (Paracoccus denitrificans (strain Pd 1222))
Explore A1BB97 
Go to UniProtKB:  A1BB97
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1BB97
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC

Query on HEC



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
N [auth B],
O [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PG6

Query on PG6



Download:Ideal Coordinates CCD File
T [auth F]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
S [auth F]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
Q [auth C],
R [auth D],
U [auth F]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A],
P [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
L [auth B],
M [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0AF
Query on 0AF
C, E
L-PEPTIDE LINKINGC11 H12 N2 O3TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.229 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.177 (Depositor) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.53α = 109.94
b = 83.52β = 91.54
c = 107.78γ = 105.78
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary