4FAS

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.206
R-Value Work: 0.165
R-Value Observed: 0.167

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/bi400960w
Primary Citation of 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.

Organizational Affiliation

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50925
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82V11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ISW Query on ISW Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain N [auth A] SDF format, chain UA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain UA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain UA [auth C]	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		Interactions Focus chain GA [auth B] Focus chain N [auth A] Focus chain UA [auth C] Interactions & Density Focus chain GA [auth B] Focus chain N [auth A] Focus chain UA [auth C]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] 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		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain LA [auth B] MOL2 format, chain LA [auth B] mmCIF format, chain LA [auth B]	LA [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Interactions & Density Focus chain LA [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain MA [auth B] MOL2 format, chain MA [auth B] mmCIF format, chain MA [auth B]	MA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Interactions & Density Focus chain MA [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain HB [auth C] SDF format, chain U [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain U [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain U [auth A]	HB [auth C], U [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain HB [auth C] Focus chain U [auth A] Interactions & Density Focus chain HB [auth C] Focus chain U [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PB [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RB [auth F] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth F] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth F] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	CB [auth C] DB [auth C] EB [auth C] FB [auth C] GB [auth C] 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		Interactions Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth F] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth F] Focus chain S [auth A] Focus chain T [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain LB [auth C] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain KB [auth C] mmCIF format, chain LB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	IB [auth C] JB [auth C] KB [auth C] LB [auth C] NA [auth B] 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		Interactions Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain MB [auth C] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain QB [auth F] MOL2 format, chain MB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth F] mmCIF format, chain MB [auth C] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth F]	MB [auth C], PA [auth B], QA [auth B], QB [auth F]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain MB [auth C] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain QB [auth F] Interactions & Density Focus chain MB [auth C] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain QB [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.206
R-Value Work: 0.165
R-Value Observed: 0.167
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Cedervall, P.E.

Wilmot, C.M.

Revision History (Full details and data files)

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