9CCK | pdb_00009cck

Multi-copper oxidase with a C-terminal cupredoxin domain from Nitrosopumilus maritimus

PDB DOI: https://doi.org/10.2210/pdb9CCK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitrosopumilus maritimus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-21 Released: 2025-02-05
Deposition Author(s): Voland, R.W., Lancaster, K.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.226 (Depositor), 0.225 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus.

Voland, R.W., Wang, H., Abruna, H.D., Lancaster, K.M.

(2025) Proc Natl Acad Sci U S A 122: e2416971122-e2416971122

PubMed: 39823305 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2416971122
Primary Citation Related Structures:
9CCK

PubMed Abstract:
Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N ₂O) emissions, although biochemical origins of this N ₂O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus . We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH ₂OH) to dioxygen (O ₂) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N ₂ via reaction with NH ₂OH and dimerization with itself to yield N ₂O. These results afford one plausible enzymatic origin for N ₂O release by AOA. Moreover, these results reveal a physiologically relevant enzymatic reaction for producing HNO, an enigmatic nitrogen oxide speculated to be operative in cellular signaling and in energy transduction.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853.

Macromolecule Content

Total Structure Weight: 510.88 kDa
Atom Count: 39,687
Modeled Residue Count: 4,508
Deposited Residue Count: 4,508
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, D, E, G A, B, D, E, G, H, J, K	409	Nitrosopumilus maritimus	Mutation(s): 0 Gene Names: Nmar_1354 EC: 1.7.2.1
UniProt
Find proteins for A9A2L1 (Nitrosopumilus maritimus (strain SCM1)) Explore A9A2L1 Go to UniProtKB: A9A2L1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9A2L1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	C, F, I, L	309	Nitrosopumilus maritimus	Mutation(s): 0 Gene Names: Nmar_1354 EC: 1.7.2.1
UniProt
Find proteins for A9A2L1 (Nitrosopumilus maritimus (strain SCM1)) Explore A9A2L1 Go to UniProtKB: A9A2L1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9A2L1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth I] SDF format, chain BA [auth D] SDF format, chain BB [auth I] SDF format, chain CA [auth D] SDF format, chain CB [auth J] SDF format, chain DA [auth D] SDF format, chain DB [auth J] SDF format, chain EA [auth D] SDF format, chain EB [auth J] SDF format, chain FA [auth E] SDF format, chain FB [auth J] SDF format, chain GA [auth E] SDF format, chain GB [auth J] SDF format, chain HA [auth E] SDF format, chain HB [auth K] SDF format, chain IA [auth E] SDF format, chain IB [auth K] SDF format, chain JA [auth E] SDF format, chain JB [auth K] SDF format, chain KA [auth F] SDF format, chain KB [auth K] SDF format, chain LA [auth F] SDF format, chain LB [auth K] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain MB [auth L] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain NB [auth L] SDF format, chain O [auth A] SDF format, chain OA [auth G] SDF format, chain OB [auth L] SDF format, chain P [auth A] SDF format, chain PA [auth G] SDF format, chain PB [auth L] SDF format, chain Q [auth A] SDF format, chain QA [auth G] SDF format, chain R [auth A] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain SA [auth G] SDF format, chain T [auth B] SDF format, chain TA [auth H] SDF format, chain U [auth B] SDF format, chain UA [auth H] SDF format, chain V [auth B] SDF format, chain VA [auth H] SDF format, chain W [auth B] SDF format, chain WA [auth H] SDF format, chain X [auth C] SDF format, chain XA [auth H] SDF format, chain Y [auth C] SDF format, chain YA [auth I] SDF format, chain Z [auth C] SDF format, chain ZA [auth I] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth J] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth J] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth J] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth K] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth K] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth K] MOL2 format, chain KA [auth F] MOL2 format, chain KB [auth K] MOL2 format, chain LA [auth F] MOL2 format, chain LB [auth K] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain MB [auth L] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain NB [auth L] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain OB [auth L] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain PB [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth I] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth I] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth J] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth J] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth J] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain GB [auth J] mmCIF format, chain HA [auth E] mmCIF format, chain HB [auth K] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth K] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth K] mmCIF format, chain KA [auth F] mmCIF format, chain KB [auth K] mmCIF format, chain LA [auth F] mmCIF format, chain LB [auth K] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain MB [auth L] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain NB [auth L] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain OB [auth L] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain PB [auth L] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth H] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth I] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth I]	AA [auth D] AB [auth I] BA [auth D] BB [auth I] CA [auth D] AA [auth D], AB [auth I], BA [auth D], BB [auth I], CA [auth D], CB [auth J], DA [auth D], DB [auth J], EA [auth D], EB [auth J], FA [auth E], FB [auth J], GA [auth E], GB [auth J], HA [auth E], HB [auth K], IA [auth E], IB [auth K], JA [auth E], JB [auth K], KA [auth F], KB [auth K], LA [auth F], LB [auth K], M [auth A], MA [auth F], MB [auth L], N [auth A], NA [auth F], NB [auth L], O [auth A], OA [auth G], OB [auth L], P [auth A], PA [auth G], PB [auth L], Q [auth A], QA [auth G], R [auth A], RA [auth G], S [auth B], SA [auth G], T [auth B], TA [auth H], U [auth B], UA [auth H], V [auth B], VA [auth H], W [auth B], WA [auth H], X [auth C], XA [auth H], Y [auth C], YA [auth I], Z [auth C], ZA [auth I]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain DA [auth D] Focus chain DB [auth J] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth E] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain HB [auth K] Focus chain IA [auth E] Focus chain IB [auth K] Focus chain JA [auth E] Focus chain JB [auth K] Focus chain KA [auth F] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth L] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth L] Focus chain O [auth A] Focus chain OA [auth G] Focus chain OB [auth L] Focus chain P [auth A] Focus chain PA [auth G] Focus chain PB [auth L] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth H] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth B] Focus chain VA [auth H] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth I] Focus chain Z [auth C] Focus chain ZA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain DA [auth D] Focus chain DB [auth J] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth E] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain HB [auth K] Focus chain IA [auth E] Focus chain IB [auth K] Focus chain JA [auth E] Focus chain JB [auth K] Focus chain KA [auth F] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth L] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth L] Focus chain O [auth A] Focus chain OA [auth G] Focus chain OB [auth L] Focus chain P [auth A] Focus chain PA [auth G] Focus chain PB [auth L] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth H] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth B] Focus chain VA [auth H] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth I] Focus chain Z [auth C] Focus chain ZA [auth I]