2IAA | pdb_00002iaa

Crystal Structure of an Electron Transfer Complex Between Aromatic Amine Dephydrogenase and Azurin from Alcaligenes Faecalis (Form 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

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This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of an Electron Transfer Complex between Aromatic Amine Dehydrogenase and Azurin from Alcaligenes faecalis.

Sukumar, N.Chen, Z.Ferrari, D.Merli, A.Rossi, G.L.Bellamy, H.D.Chistoserdov, A.Davidson, V.L.Mathews, F.S.

(2006) Biochemistry 45: 13500-13510

  • DOI: https://doi.org/10.1021/bi0612972
  • Primary Citation Related Structures: 
    2H3X, 2H47, 2IAA

  • PubMed Abstract: 

    The crystal structure of an electron transfer complex of aromatic amine dehydrogenase (AADH) and azurin is presented. Electrons are transferred from the tryptophan tryptophylquinone (TTQ) cofactor of AADH to the type I copper of the cupredoxin azurin. This structure is compared with the complex of the TTQ-containing methylamine dehydrogenase (MADH) and the cupredoxin amicyanin. Despite significant similarities between the two quinoproteins and the two cupredoxins, each is specific for its respective partner and the ionic strength dependence and magnitude of the binding constant for each complex are quite different. The AADH-azurin interface is largely hydrophobic, covering approximately 500 A(2) of surface on each molecule, with one direct hydrogen bond linking them. The closest distance from TTQ to copper is 12.6 A compared with a distance of 9.3 A in the MADH-amicyanin complex. When the MADH-amicyanin complex is aligned with the AADH-azurin complex, the amicyanin lies on top of the azurin but is oriented quite differently. Although the copper atoms differ in position by approximately 4.7 A, the amicyanin bound to MADH appears to be rotated approximately 90 degrees from its aligned position with azurin. Comparison of the structures of the two complexes identifies features of the interface that dictate the specificity of the protein-protein interaction and determine the rate of interprotein electron transfer.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 65211, USA.

Macromolecule Content 

  • Total Structure Weight: 128.77 kDa 
  • Atom Count: 9,307 
  • Modeled Residue Count: 1,072 
  • Deposited Residue Count: 1,178 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aromatic Amine Dehydrogenase
A, D
390Alcaligenes faecalisMutation(s): 0 
EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
UniProt
Find proteins for P84888 (Alcaligenes faecalis)
Explore P84888 
Go to UniProtKB:  P84888
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84888
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Aromatic Amine Dehydrogenase
B, E
135Alcaligenes faecalisMutation(s): 0 
EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
UniProt
Find proteins for P84887 (Alcaligenes faecalis)
Explore P84887 
Go to UniProtKB:  P84887
Entity Groups
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UniProt GroupP84887
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Azurin128Alcaligenes faecalisMutation(s): 0 
UniProt
Find proteins for P00281 (Alcaligenes faecalis)
Explore P00281 
Go to UniProtKB:  P00281
Entity Groups
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UniProt GroupP00281
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU

Query on CU



Download:Ideal Coordinates CCD File
F [auth C]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TRQ
Query on TRQ
B, E
L-PEPTIDE LINKINGC11 H10 N2 O4TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.216α = 90
b = 131.722β = 90
c = 133.204γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary