7AQA

Pseudomonas stutzeri nitrous oxide reductase mutant, H382A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase.

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

(2021) Chem Sci 12: 3239-3244

  • DOI: https://doi.org/10.1039/d0sc05204c
  • Primary Citation of Related Structures:  
    6Y6Y, 6Y71, 6Y72, 6Y77, 6Y7D, 6Y7E, 7AQA

  • PubMed Abstract: 

    Nitrous oxide reductase (N 2 OR) is the only known enzyme reducing environmentally critical nitrous oxide (N 2 O) to dinitrogen (N 2 ) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster Cu Z remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N 2 OR in Escherichia coli . While no copper ion was found in the Cu Z binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, S Z2 , had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of S Z2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in Cu Z and is thus of high mechanistic interest.


  • Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrous-oxide reductase
A, B
646Stutzerimonas stutzeriMutation(s): 1 
Gene Names: nosZ
EC: 1.7.2.4
UniProt
Find proteins for P19573 (Stutzerimonas stutzeri)
Explore P19573 
Go to UniProtKB:  P19573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19573
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K7E (Subject of Investigation/LOI)
Query on K7E

Download Ideal Coordinates CCD File 
C [auth A]sulfanyl-(tricuprio-$l^{4}-sulfanyl)copper
Cu4 H S2
HNDPNHLKTCWFEP-UHFFFAOYSA-M
B3P
Query on B3P

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
RUQ (Subject of Investigation/LOI)
Query on RUQ

Download Ideal Coordinates CCD File 
L [auth B](dicuprio-$l^{3}-sulfanyl)-sulfanyl-copper
Cu3 H S2
GESPGIVOECOYJT-UHFFFAOYSA-M
PHE
Query on PHE

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K [auth B]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
CUA
Query on CUA

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J [auth A],
R [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
FMT
Query on FMT

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P [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA
Query on CA

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F [auth A],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

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G [auth A],
O [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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H [auth A],
I [auth A],
Q [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.824α = 90
b = 76.834β = 93.47
c = 108.513γ = 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  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 2.0: 2021-07-07
    Changes: Database references, Non-polymer description
  • Version 2.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description