4FAS | pdb_00004fas

Complex crystal structure of hydroxylamine oxidoreductase and NE1300 from Nitrosomonas europaea

• PDB DOI: https://doi.org/10.2210/pdb4FAS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitrosomonas europaea ATCC 19718
• Mutation(s): No 


• Deposited: 2012-05-22 Released: 2013-09-04 
• Deposition Author(s): Cedervall, P.E., Wilmot, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structural studies of hydroxylamine oxidoreductase reveal a unique heme cofactor and a previously unidentified interaction partner.

Cedervall, P.E., Hooper, A.B., Wilmot, C.M.

(2013) Biochemistry 52: 6211-6218

• PubMed: 23952581 
• DOI: https://doi.org/10.1021/bi400960w
• Primary Citation Related Structures: 
  4FAS


• PubMed Abstract: 
  

  Hydroxylamine oxidoreductase (HAO) is a 24-heme homotrimeric enzyme that catalyzes the conversion of hydroxylamine to nitrite in nitrifying bacteria: a key reaction in the nitrogen cycle. One heme in each HAO monomer is a highly unusual heme P460 that is the site of catalysis. This was proposed to be a c-type heme that contained an additional porphyrin-tyrosine cross-link. Here, we report the crystal structure of HAO from Nitrosomonas europaea to 2.1 Å resolution that defines a different model compatible with the crystallographic and biochemical data. The structure reveals that heme P460 contains two covalent cross-links between the porphyrin and a Tyr residue. In addition, the enzyme was purified from source, and an unknown physiological HAO binding partner was present within the crystal (annotated in the genome as hypothetical protein NE1300). NE1300 may play a structural role in the ternary complex with cytochrome c554, the physiological electron acceptor of HAO.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 226.15 kDa 
• Atom Count: 15,197 
• Modeled Residue Count: 1,653 
• Deposited Residue Count: 1,845 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxylamine oxidoreductase	A, B, C	546	Nitrosomonas europaea ATCC 19718	Mutation(s): 0  EC: 1.7.3.4 (PDB Primary Data), 1.7.2.6 (UniProt), 1.7.2.9 (UniProt)
UniProt
Find proteins for Q50925 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q50925  Go to UniProtKB:  Q50925

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NE1300	D, E, F	69	Nitrosomonas europaea ATCC 19718	Mutation(s): 0
UniProt
Find proteins for Q82V11 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82V11  Go to UniProtKB:  Q82V11

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ISW	GA [auth B], N [auth A], UA [auth C]	{3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~]dipropanoato(2-)}iron C34 H34 Fe N4 O4 QSWMAEGFLATCMU-JMAPEOGHSA-L
HEC	AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], DA [auth B], EA [auth B], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], VA [auth C], WA [auth C], XA [auth C], YA [auth C], Z [auth B], ZA [auth C]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
P6G	LA [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	MA [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	HB [auth C], U [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HA [auth B], IA [auth B], JA [auth B], KA [auth B], O [auth A], P [auth A], PB [auth C], Q [auth A], R [auth A], RB [auth F], S [auth A], T [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	IB [auth C], JB [auth C], KB [auth C], LB [auth C], NA [auth B], NB [auth C], OA [auth B], OB [auth C], RA [auth B], SA [auth B], TA [auth B], V [auth A], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	MB [auth C], PA [auth B], QA [auth B], QB [auth F]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.731	α = 90
b = 142.618	β = 90
c = 107.376	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Cedervall, P.E., Wilmot, C.M.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-11-20
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary