1MDA

CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.285 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of an electron-transfer complex between methylamine dehydrogenase and amicyanin.

Chen, L., Durley, R., Poliks, B.J., Hamada, K., Chen, Z., Mathews, F.S., Davidson, V.L., Satow, Y., Huizinga, E., Vellieux, F.M., Hol, W.G.J.

(1992) Biochemistry 31: 4959-4964

  • DOI: 10.1021/bi00136a006
  • Primary Citation of Related Structures:  
    1MDA

  • PubMed Abstract: 

    • The crystal structure of the complex between the quinoprotein methylamine dehydrogenase (MADH) and the type I blue copper protein amicyanin, both from Paracoccus denitrificans, has been determined at 2.5-A resolution using molecular replacement. The search model was MADH from Thiobacillus versutus ...

    The crystal structure of the complex between the quinoprotein methylamine dehydrogenase (MADH) and the type I blue copper protein amicyanin, both from Paracoccus denitrificans, has been determined at 2.5-A resolution using molecular replacement. The search model was MADH from Thiobacillus versutus. The amicyanin could be located in an averaged electron density difference map and the model improved by refinement and model building procedures. Nine beta-strands are observed within the amicyanin molecule. The copper atom is located between three antiparallel strands and is about 2.5 A below the protein surface. The major intermolecular interactions occur between amicyanin and the light subunit of MADH where the interface is largely hydrophobic. The copper atom of amicyanin and the redox cofactor of MADH are about 9.4 A apart. One of the copper ligands, His 95, lies between the two redox centers and may facilitate electron transfer between them.

    Related Citations: 
    • Three-Dimensional Structure of the Quinoprotein Methylamine Dehydrogenase from Paracoccus Denitrificans Determined by Molecular Replacement at 2.8 Angstroms Resolution
      Chen, L., Mathews, F.S., Davidson, V.L., Huizinga, E.G., Vellieux, F.M.D., Hol, W.G.J.
      (1992) Proteins 14: 288
    • A New Cofactor in a Prokaryotic Enzyme: Tryptophan Tryptophylquinone as the Redox Prosthetic Group in Methylamine Dehydrogenase
      Mcintire, W.S., Wemmer, D.E., Chistoserdov, A., Lidstrom, M.E.
      (1991) Science 252: 817
    • Structure of Quinoprotein Methylamine Dehydrogenase at 2.25 Angstroms Resolution
      Vellieux, F.M.D., Huitema, F., Groendijk, H., Kalk, K.H., Frank Jzn., J., Jongejan, J.A., Duine, J.A., Petratos, K., Drenth, J., Hol, W.G.J.
      (1989) EMBO J 8: 2171
    • Structure Determination of Quinoprotein Methylamine Dehydrogenase from Thiobacillus Versutus
      Vellieux, F.M.D., Kalk, K.H., Drenth, J., Hol, W.G.
      (1990) Acta Crystallogr B 46: 806
    Organizational Affiliation: 

    Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)A [auth H], C [auth J]368Paracoccus denitrificansMutation(s): 0 
EC: 1.4.99.3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)B [auth L], D [auth M]121Paracoccus denitrificansMutation(s): 0 
EC: 1.4.99.3
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AMICYANINE [auth A], F [auth B]103Paracoccus denitrificansMutation(s): 0 
Gene Names: mauC, ami
UniProt
Find proteins for P22364 (Paracoccus denitrificans)
Explore P22364 
Go to UniProtKB:  P22364
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU
Download Ideal Coordinates CCD File 
G [auth A], H [auth B]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRQ
Query on TRQ		B [auth L], D [auth M]L-PEPTIDE LINKINGC11 H10 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.285 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.7α = 90
b = 124.7β = 90
c = 247.4γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance