9F8X | pdb_00009f8x

Low-dose structure of Marinobacter nauticus nitrous oxide reductase

PDB DOI: https://doi.org/10.2210/pdb9F8X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Marinobacter nauticus
Mutation(s): Yes

Deposited: 2024-05-07 Released: 2024-06-19
Deposition Author(s): Einsle, O., Pomowski, A.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC), Foundation for Science and Technology (FCT), European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.152 (Depositor), 0.152 (DCC)
R-Value Work:
0.130 (Depositor), 0.130 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Revisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticus.

Pomowski, A., Dell'Acqua, S., Wust, A., Pauleta, S.R., Moura, I., Einsle, O.

(2024) J Biol Inorg Chem 29: 279-290

PubMed: 38720157 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s00775-024-02056-y
Primary Citation Related Structures:
9F8X

PubMed Abstract:
Copper-containing nitrous oxide reductase catalyzes a 2-electron reduction of the green-house gas N ₂O to yield N ₂. It contains two metal centers, the binuclear electron transfer site Cu _A, and the unique, tetranuclear Cu _Z center that is the site of substrate binding. Different forms of the enzyme were described previously, representing variations in oxidation state and composition of the metal sites. Hypothesizing that many reported discrepancies in the structural data may be due to radiation damage during data collection, we determined the structure of anoxically isolated Marinobacter nauticus N ₂OR from diffraction data obtained with low-intensity X-rays from an in-house rotating anode generator and an image plate detector. The data set was of exceptional quality and yielded a structure at 1.5 Å resolution in a new crystal form. The Cu _A site of the enzyme shows two distinct conformations with potential relevance for intramolecular electron transfer, and the Cu _Z cluster is present in a [4Cu:2S] configuration. In addition, the structure contains three additional types of ions, and an analysis of anomalous scattering contributions confirms them to be Ca ²⁺, K ⁺, and Cl ^-. The uniformity of the present structure supports the hypothesis that many earlier analyses showed inhomogeneities due to radiation effects. Adding to the earlier description of the same enzyme with a [4Cu:S] Cu _Z site, a mechanistic model is presented, with a structurally flexible Cu _Z center that does not require the complete dissociation of a sulfide prior to N ₂O binding.

Organizational Affiliation

Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 284.96 kDa
Atom Count: 21,756
Modeled Residue Count: 2,288
Deposited Residue Count: 2,524
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrous-oxide reductase	A, B, C, D	631	Marinobacter nauticus	Mutation(s): 3 EC: 1.7.2.4
UniProt
Find proteins for A0A368XMX8 (Marinobacter nauticus) Explore A0A368XMX8 Go to UniProtKB: A0A368XMX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A368XMX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CUK (Subject of Investigation/LOI) Query on CUK Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain IA [auth D] SDF format, chain F [auth A] SDF format, chain AA [auth C] MOL2 format, chain M [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain M [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth C]	AA [auth C], F [auth A], IA [auth D], M [auth B]	[4Cu:2S] cluster Cu₄ S₂ PDBAWKBNXYUXTL-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain IA [auth D] Focus chain M [auth B] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain IA [auth D] Focus chain M [auth B]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain L [auth B] SDF format, chain HA [auth D] SDF format, chain E [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain L [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain L [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain E [auth A]	E [auth A], HA [auth D], L [auth B], Z [auth C]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth D] Focus chain L [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain HA [auth D] Focus chain L [auth B] Focus chain Z [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain NA [auth D] SDF format, chain MA [auth D] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C]	EA [auth C] FA [auth C] GA [auth C] J [auth A] K [auth A] EA [auth C], FA [auth C], GA [auth C], J [auth A], K [auth A], MA [auth D], NA [auth D], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain LA [auth D] SDF format, chain JA [auth D] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth C] SDF format, chain BA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] DA [auth C] G [auth A] I [auth A] JA [auth D] BA [auth C], DA [auth C], G [auth A], I [auth A], JA [auth D], LA [auth D], N [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain N [auth B] Focus chain P [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain N [auth B] Focus chain P [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain KA [auth D] SDF format, chain H [auth A] SDF format, chain CA [auth C] MOL2 format, chain O [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain CA [auth C] mmCIF format, chain O [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain CA [auth C]	CA [auth C], H [auth A], KA [auth D], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain H [auth A] Focus chain KA [auth D] Focus chain O [auth B] Interactions & Density Focus chain CA [auth C] Focus chain H [auth A] Focus chain KA [auth D] Focus chain O [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B]	Q [auth B], R [auth B], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.152 (Depositor), 0.152 (DCC)
R-Value Work: 0.130 (Depositor), 0.130 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.26	α = 81.384
b = 69.375	β = 77.918
c = 153.188	γ = 88.608

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Einsle, O.

Pomowski, A.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	235777276
German Research Foundation (DFG)	Germany	311061829
European Research Council (ERC)	European Union	310656
Foundation for Science and Technology (FCT)	Portugal	UIDP/04378/2020
Foundation for Science and Technology (FCT)	Portugal	UIDB/04378/2020
Foundation for Science and Technology (FCT)	Portugal	LA/P/0140/2020
Foundation for Science and Technology (FCT)	Portugal	UIDB/50006/2020
Foundation for Science and Technology (FCT)	Portugal	UIDP/50006/2020
Foundation for Science and Technology (FCT)	Portugal	2022.01152.PTDC
European Molecular Biology Organization (EMBO)	European Union	ASTF 282.00-2010