7OG7 | pdb_00007og7

Crystal structure of the copper chaperone NosL from Shewanella denitrificans

PDB DOI: https://doi.org/10.2210/pdb7OG7/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Shewanella denitrificans OS217
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-06 Released: 2021-07-07
Deposition Author(s): Prasser, B., Schoener, L., Zhang, L., Einsle, O.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.222 (Depositor), 0.221 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Copper Chaperone NosL Forms a Heterometal Site for Cu Delivery to Nitrous Oxide Reductase.

Prasser, B., Schoner, L., Zhang, L., Einsle, O.

(2021) Angew Chem Int Ed Engl 60: 18810-18814

PubMed: 34171184 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202106348
Primary Citation Related Structures:
7OG7

PubMed Abstract:
The final step of denitrification is the reduction of nitrous oxide (N ₂ O) to N ₂ , mediated by Cu-dependent nitrous oxide reductase (N ₂ OR). Its metal centers, Cu _A and Cu _Z , are assembled through sequential provision of twelve Cu ^I ions by a metallochaperone that forms part of a nos gene cluster encoding the enzyme and its accessory factors. The chaperone is the nosL gene product, an 18 kDa lipoprotein predicted to reside in the outer membrane of Gram-negative bacteria. In order to better understand the assembly of N ₂ OR, we have produced NosL from Shewanella denitrificans and determined the structure of the metal-loaded chaperone by X-ray crystallography. The protein assembled a heterodinuclear metal site consisting of Zn ^II and Cu ^I , as evidenced by anomalous X-ray scattering. While only Cu ^I is delivered to the enzyme, the stabilizing presence of Zn ^II is essential for the functionality and structural integrity of the chaperone.

Organizational Affiliation

Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.

Macromolecule Content

Total Structure Weight: 20.65 kDa
Atom Count: 1,188
Modeled Residue Count: 134
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NosL	A	182	Shewanella denitrificans OS217	Mutation(s): 0 Gene Names: Sden_2215
UniProt
Find proteins for Q12M31 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12M31 Go to UniProtKB: Q12M31
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12M31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CU1 (Subject of Investigation/LOI) Query on CU1 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CCN Query on CCN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	ACETONITRILE C₂ H₃ N WEVYAHXRMPXWCK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]