6RKZ

Recombinant Pseudomonas stutzeri nitrous oxide reductase, form II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Functional assembly of nitrous oxide reductase provides insights into copper site maturation.

Zhang, L., Wust, A., Prasser, B., Muller, C., Einsle, O.

(2019) Proc Natl Acad Sci U S A 116: 12822-12827

  • DOI: 10.1073/pnas.1903819116
  • Primary Citation of Related Structures:  
    6RKZ, 6RL0

  • PubMed Abstract: 

    • The multicopper enzyme nitrous oxide reductase reduces the greenhouse gas N 2 O to uncritical N 2 as the final step of bacterial denitrification. Its two metal centers require an elaborate assembly machinery that so far has precluded heterologous production as a prerequisite for bioremediatory applications in agriculture and wastewater treatment ...

    The multicopper enzyme nitrous oxide reductase reduces the greenhouse gas N 2 O to uncritical N 2 as the final step of bacterial denitrification. Its two metal centers require an elaborate assembly machinery that so far has precluded heterologous production as a prerequisite for bioremediatory applications in agriculture and wastewater treatment. Here, we report on the production of active holoenzyme in Escherichia coli using a two-plasmid system to produce the entire biosynthetic machinery as well as the structural gene for the enzyme. Using this recombinant system to probe the role of individual maturation factors, we find that the ABC transporter NosFY and the accessory NosD protein are essential for the formation of the [4Cu:2S] site Cu Z , but not the electron transfer site Cu A Depending on source organism, the heterologous host E. coli can, in some cases, compensate for the lack of the Cu chaperone NosL, while in others this protein is strictly required, underlining the case for designing a recombinant system to be entirely self-contained.

    Organizational Affiliation: 

    BIOSS Centre for Biological Signalling Studies, 79104 Freiburg, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrous-oxide reductaseA, B646Pseudomonas stutzeriMutation(s): 0 
Gene Names: nosZ
EC: 1.7.2.4
UniProt
Find proteins for P19573 (Pseudomonas stutzeri)
Explore P19573 
Go to UniProtKB:  P19573
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUZ
Query on CUZ
Download Ideal Coordinates CCD File 
 O [auth A], Y [auth B](MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Cu4 S
IGIWMDIIFLPFOP-UHFFFAOYSA-N		 Ligand Interaction
B3P
Query on B3P
Download Ideal Coordinates CCD File 
 C [auth A], Q [auth B]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N		 Ligand Interaction
CUA
Query on CUA
Download Ideal Coordinates CCD File 
 P [auth A], Z [auth B]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , U [auth B] , V [auth B] , 
G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  U [auth B],  V [auth B],  W [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
 E [auth A], S [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
 F [auth A], T [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
 M [auth A], N [auth A], X [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
 D [auth A], R [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.887α = 90
b = 76.789β = 93.33
c = 108.823γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
AutoPROCdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilGermany310656

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references