1MG2

MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

MUTATION OF AlPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN

Sun, D.Chen, Z.W.Mathews, F.S.Davidson, V.L.

(2002) Biochemistry 41: 13926-13933

  • DOI: 10.1021/bi026654x
  • Primary Citation of Related Structures:  
    1MG2, 1MG3

  • PubMed Abstract: 
  • Methylamine dehydrogenase (MADH) possesses an alpha(2)beta(2) structure with each smaller beta subunit possessing a tryptophan tryptophylquinone (TTQ) prosthetic group. Phe55 of the alpha subunit is located where the substrate channel from the enzyme surface opens into the active site ...

    Methylamine dehydrogenase (MADH) possesses an alpha(2)beta(2) structure with each smaller beta subunit possessing a tryptophan tryptophylquinone (TTQ) prosthetic group. Phe55 of the alpha subunit is located where the substrate channel from the enzyme surface opens into the active site. Site-directed mutagenesis of alphaPhe55 has revealed roles for this residue in determining substrate specificity and binding monovalent cations at the active site. It is now shown that the alphaF55A mutation also increases the rate of the true electron transfer (ET) reaction from O-quinol MADH to amicyanin. The reorganization energy associated with the ET reaction is decreased from 2.3 to 1.8 eV. The electronic coupling associated with the ET reaction is decreased from 12 to 3 cm(-1). The crystal structure of alphaF55A MADH in complex with its electron acceptors, amicyanin and cytochrome c-551i, has been determined. Little difference in the overall structure is seen, relative to the native complex; however, there are significant changes in the solvent content of the active site and substrate channel. The crystal structure of alphaF55A MADH has also been determined with phenylhydrazine covalently bound to TTQ in the active site. Phenylhydrazine binding significantly perturbs the orientation of the TTQ rings relative to each other. The ET results are discussed in the context of the new and old crystal structures of the native and mutant enzymes.


    Related Citations: 
    • Structureof an electron transfer complex: methylamine dehydrogenase, amicyanin, and cytochrome c551i.
      Chen, L., Durley, R., Mathews, F.S., Davidson, V.L.
      (1994) Science 264: 86

    Organizational Affiliation

    Department of Biochemistry, The University of Mississippi Medical Center, Jackson, Mississippi 39216-4505, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methylamine dehydrogenase, heavy chain AEIM390Paracoccus denitrificansMutation(s): 1 
Gene Names: mauB
EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
Find proteins for P29894 (Paracoccus denitrificans)
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Go to UniProtKB:  P29894
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methylamine dehydrogenase, light chain BFJN131Paracoccus denitrificansMutation(s): 1 
Gene Names: mauA
EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
Find proteins for P22619 (Paracoccus denitrificans)
Explore P22619 
Go to UniProtKB:  P22619
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Amicyanin CGKO105Paracoccus denitrificansMutation(s): 0 
Gene Names: mauCami
Find proteins for P22364 (Paracoccus denitrificans)
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Go to UniProtKB:  P22364
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C-L DHLP155Paracoccus denitrificansMutation(s): 0 
Gene Names: moxG
Find proteins for P29899 (Paracoccus denitrificans)
Explore P29899 
Go to UniProtKB:  P29899
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
D, H, L, P
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
A, B, E, F, I, J, M, N
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CU
Query on CU

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C, G, K, O
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D, H, L, P
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRQ
Query on TRQ
B,F,J,NL-PEPTIDE LINKINGC11 H10 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.122α = 90
b = 188.201β = 99.24
c = 127.1γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary