Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 146.03 kDa 
• Atom Count: 10253 
• Modelled Residue Count: 1172 
• Deposited Residue Count: 1292 
• Unique protein chains: 1

6RKZ

Recombinant Pseudomonas stutzeri nitrous oxide reductase, form II

• PDB DOI: 10.2210/pdb6RKZ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Pseudomonas stutzeri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-30 Released: 2019-06-26 
• Deposition Author(s): Zhang, L., Wuest, A., Prasser, B., Mueller, C., Einsle, O.
• Funding Organization(s): European Research Council

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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 

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

• PubMed: 31189605 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrous-oxide reductase	A, B	646	Pseudomonas stutzeri	Mutation(s): 0  Gene Names: nosZ EC: 1.7.2.4
UniProt
Find proteins for P19573 (Pseudomonas stutzeri) Explore P19573  Go to UniProtKB:  P19573

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CUZ (Subject of Investigation/LOI)	O [auth A], Y [auth B]	(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION Cu4 S IGIWMDIIFLPFOP-UHFFFAOYSA-N
B3P	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
CUA	P [auth A], Z [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
FMT	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
CA	E [auth A], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	F [auth A], T [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	M [auth A], N [auth A], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 68.887	α = 90
b = 76.789	β = 93.33
c = 108.823	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
AutoPROC	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-30 
• Released Date: 2019-06-26 
Deposition Author(s): Zhang, L., Wuest, A., Prasser, B., Mueller, C., Einsle, O.

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Funding Organization	Location	Grant Number
European Research Council	Germany	310656

Revision History  

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