7AQ7

Pseudomonas stutzeri nitrous oxide reductase mutant, H583Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report



Literature

Histidine-Gated Proton-Coupled Electron Transfer to the Cu A Site of Nitrous Oxide Reductase.

Zhang, L.Bill, E.Kroneck, P.M.H.Einsle, O.

(2020) J Am Chem Soc 

  • DOI: 10.1021/jacs.0c10057
  • Primary Citation of Related Structures:  
    7AQ8, 7AQ7, 7APY, 7AQ9, 7AQ0, 7AQ2, 7AQ4, 7AQ3, 7AQ6, 7AQ5

  • PubMed Abstract: 
  • Copper-containing nitrous oxide reductase (N 2 OR) is the only known enzyme to catalyze the conversion of the environmentally critical greenhouse gas nitrous oxide (N 2 O) to dinitrogen (N 2 ) as the final step of bac ...

    Copper-containing nitrous oxide reductase (N 2 OR) is the only known enzyme to catalyze the conversion of the environmentally critical greenhouse gas nitrous oxide (N 2 O) to dinitrogen (N 2 ) as the final step of bacterial denitrification. Other than its unique tetranuclear active site Cu Z , the binuclear electron entry point Cu A is also utilized in other enzymes, including cytochrome c oxidase. In the Cu A site of Pseudomonas stutzeri N 2 OR, a histidine ligand was found to undergo a conformational flip upon binding of the substrate N 2 O between the two copper centers. Here we report on the systematic mutagenesis and spectroscopic and structural characterization of this histidine and surrounding H-bonding residues, based on an established functional expression system for Ps N 2 OR in E. coli . A single hydrogen bond from Ser550 is sufficient to stabilize an unbound conformation of His583, as shown in a Asp576Ala variant, while the additional removal of the hydrogen bond in a Asp576Ala/Ser550Ala double variant compelled His583 to stay in a bound conformation as a ligand to Cu A . Systematic mutagenesis of His583 to Ala, Asp, Asn, Glu, Gln, Lys, Phe, Tyr, and Trp showed that although both the Cu Z and Cu A sites were present in all the variants, only the ones with a protonable side chain, i.e., His, Asp, and Glu, were able to mediate electron transfer at physiological pH. This observation is in line with a proton-coupled electron transfer mechanism at the Cu A site of N 2 OR.


    Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrous-oxide reductaseAB646Pseudomonas stutzeriMutation(s): 1 
Gene Names: nosZ
EC: 1.7.2.4
Find proteins for P19573 (Pseudomonas stutzeri)
Explore P19573 
Go to UniProtKB:  P19573
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUZ
Query on CUZ

Download Ideal Coordinates CCD File 
A, B
(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Cu4 S
IGIWMDIIFLPFOP-UHFFFAOYSA-N
 Ligand Interaction
B3P
Query on B3P

Download Ideal Coordinates CCD File 
A, 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 
A, B
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.734α = 90
b = 76.071β = 93.49
c = 108.467γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany310656
German Research Foundation (DFG)Germany192904750

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release