4RWM

Kuenenia stuttgartiensis hydroxylamine oxidoreductase cryoprotected with ethylene glycol

PDB DOI: https://doi.org/10.2210/pdb4RWM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candidatus Kuenenia stuttgartiensis
Mutation(s): No

Deposited: 2014-12-05 Released: 2015-08-12
Deposition Author(s): Dietl, A., Maalcke, W., Barends, T.R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.164
R-Value Work: 0.147
R-Value Observed: 0.148

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

An unexpected reactivity of the P460 cofactor in hydroxylamine oxidoreductase.

Dietl, A., Maalcke, W., Barends, T.R.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1708-1713

PubMed: 26249351 Search on PubMed
DOI: https://doi.org/10.1107/S1399004715010706
Primary Citation of Related Structures:
4RWM

PubMed Abstract:
Hydroxylamine oxidoreductases (HAOs) contain a unique haem cofactor called P460 that consists of a profoundly ruffled c-type haem with two covalent bonds between the haem porphyrin and a conserved tyrosine. This cofactor is exceptional in that it abstracts electrons from a ligand bound to the haem iron, whereas other haems involved in redox chemistry usually inject electrons into their ligands. The effects of the tyrosine cross-links and of the haem ruffling on the chemistry of this cofactor have been investigated theoretically but are not yet clear. A new crystal structure of an HAO from Candidatus Kuenenia stuttgartiensis, a model organism for anaerobic ammonium oxidation, now shows that its P460 cofactor has yet another unexpected reactivity: when ethylene glycol was used as a cryoprotectant, the 1.8 ? resolution electron-density maps showed additional density which could be interpreted as an ethylene glycol molecule covalently bound to the C16 atom of the haem ring, opposite the covalent links to the conserved tyrosine. Possible causes for this unexpected reactivity are discussed.

Organizational Affiliation

Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 62.46 kDa
Atom Count: 4,845
Modelled Residue Count: 497
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Similar to hydroxylamine oxidoreductase hao	A	500	Candidatus Kuenenia stuttgartiensis	Mutation(s): 0 EC: 1.7.3.4 (PDB Primary Data), 1.7.2.9 (UniProt)
UniProt
Find proteins for Q1PX48 (Kuenenia stuttgartiensis) Explore Q1PX48 Go to UniProtKB: Q1PX48
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1PX48
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
HG1 Query on HG1 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	1-[(4-cyclohexylbutanoyl)(2-hydroxyethyl)amino]-1-deoxy-D-glucitol C₁₈ H₃₅ N O₇ XAMJEPWYNXYYBT-BURFUSLBSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.164
R-Value Work: 0.147
R-Value Observed: 0.148
Space Group: P 2₁ 3

Unit Cell:

Length ( ? )	Angle ( ? )
a = 130.29	α = 90
b = 130.29	β = 90
c = 130.29	γ = 90

Software Package:

Software Name	Purpose
HEIDI	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Dietl, A.

Maalcke, W.

Barends, T.R.M.

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2017-10-25
Changes: Author supporting evidence
Version 1.2: 2018-05-16
Changes: Data collection, Database references
Version 2.0: 2021-03-10
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-11-06
Changes: Data collection, Database references, Structure summary

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4RWM

Kuenenia stuttgartiensis hydroxylamine oxidoreductase cryoprotected with ethylene glycol

An unexpected reactivity of the P460 cofactor in hydroxylamine oxidoreductase.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)