3LB8

Crystal structure of the covalent putidaredoxin reductase-putidaredoxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 

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Literature

Crystal structure of the putidaredoxin reductase x putidaredoxin electron transfer complex.

Sevrioukova, I.F.Poulos, T.L.Churbanova, I.Y.

(2010) J Biol Chem 285: 13616-13620

  • DOI: 10.1074/jbc.M110.104968
  • Primary Citation of Related Structures:  
    3LB8

  • PubMed Abstract: 
  • In the camphor monooxygenase system from Pseudomonas putida, the [2Fe-2S]-containing putidaredoxin (Pdx) shuttles electrons between the NADH-dependent putidaredoxin reductase (Pdr) and cytochrome P450(cam). The mechanism of the Pdr.Pdx redox couple has been investigated by a variety of techniques ...

    In the camphor monooxygenase system from Pseudomonas putida, the [2Fe-2S]-containing putidaredoxin (Pdx) shuttles electrons between the NADH-dependent putidaredoxin reductase (Pdr) and cytochrome P450(cam). The mechanism of the Pdr.Pdx redox couple has been investigated by a variety of techniques. One of the exceptions is x-ray crystallography as the native partners associate weakly and resist co-crystallization. Here, we present the 2.6-A x-ray structure of a catalytically active complex between Pdr and Pdx C73S/C85S chemically cross-linked via the Lys(409Pdr)-Glu(72Pdx) pair. The 365 A(2) Pdr-Pdx interface is predominantly hydrophobic with one central Arg(310Pdr)-Asp(38Pdx) salt bridge, likely assisting docking and orienting the partners optimally for electron transfer, and a few peripheral hydrogen bonds. A predicted 12-A-long electron transfer route between FAD and [2Fe-2S] includes flavin flanking Trp(330Pdr) and the iron ligand Cys(39Pdx). The x-ray model agrees well with the experimental and theoretical results and suggests that the linked Pdx must undergo complex movements during turnover to accommodate P450(cam), which could limit the Pdx-to-P450(cam) electron transfer reaction.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA. sevrioui@uci.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putidaredoxin reductaseA, B436Pseudomonas putidaMutation(s): 0 
Gene Names: camA
EC: 1.18.1 (PDB Primary Data), 1.18.1.5 (UniProt)
UniProt
Find proteins for P16640 (Pseudomonas putida)
Explore P16640 
Go to UniProtKB:  P16640
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16640
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PutidaredoxinC, D106Pseudomonas putidaMutation(s): 2 
Gene Names: camAcamB
UniProt
Find proteins for P00259 (Pseudomonas putida)
Explore P00259 
Go to UniProtKB:  P00259
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00259
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
G [auth C],
H [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.6α = 90
b = 103.4β = 90
c = 167.7γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations