9CCK | pdb_00009cck

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


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

  • DOI: https://doi.org/10.1073/pnas.2416971122
  • Primary Citation of 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 2 O) emissions, although biochemical origins of this N 2 O 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 2 OH) to dioxygen (O 2 ) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N 2 via reaction with NH 2 OH and dimerization with itself to yield N 2 O. These results afford one plausible enzymatic origin for N 2 O 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase
A, B, D, E, G
A, B, D, E, G, H, J, K
409Nitrosopumilus maritimusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9A2L1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase
C, F, I, L
309Nitrosopumilus maritimusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9A2L1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.292α = 90
b = 92.976β = 95.791
c = 204.483γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124908

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release