1D6U | pdb_00001d6u

CRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE

PDB DOI: https://doi.org/10.2210/pdb1D6U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1999-10-15 Released: 2000-02-02
Deposition Author(s): Wilmot, C.M., Hajdu, J., McPherson, M.J., Knowles, P.F., Phillips, S.E.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.239 (Depositor), 0.235 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Visualization of dioxygen bound to copper during enzyme catalysis.

Wilmot, C.M., Hajdu, J., McPherson, M.J., Knowles, P.F., Phillips, S.E.

(1999) Science 286: 1724-1728

PubMed: 10576737 Search on PubMed
DOI: https://doi.org/10.1126/science.286.5445.1724
Primary Citation Related Structures:
1D6U, 1D6Y, 1D6Z

PubMed Abstract:
X-ray crystal structures of three species related to the oxidative half of the reaction of the copper-containing quinoprotein amine oxidase from Escherichia coli have been determined. Crystals were freeze-trapped either anaerobically or aerobically after exposure to substrate, and structures were determined to resolutions between 2.1 and 2.4 angstroms. The oxidation state of the quinone cofactor was investigated by single-crystal spectrophotometry. The structures reveal the site of bound dioxygen and the proton transfer pathways involved in oxygen reduction. The quinone cofactor is regenerated from the iminoquinone intermediate by hydrolysis involving Asp383, the catalytic base in the reductive half-reaction. Product aldehyde inhibits the hydrolysis, making release of product the rate-determining step of the reaction in the crystal.

Organizational Affiliation

Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

Macromolecule Content

Total Structure Weight: 163.57 kDa
Atom Count: 12,855
Modeled Residue Count: 1,438
Deposited Residue Count: 1,454
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER AMINE OXIDASE	A, B	727	Escherichia coli	Mutation(s): 1 EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for P46883 (Escherichia coli (strain K12)) Explore P46883 Go to UniProtKB: P46883
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEA Query on PEA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-PHENYLETHYLAMINE C₈ H₁₂ N BHHGXPLMPWCGHP-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
HY1 Query on HY1 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	PHENYLACETALDEHYDE C₈ H₈ O DTUQWGWMVIHBKE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYQ Query on TYQ	A, B	L-PEPTIDE LINKING	C₉ H₁₂ N₂ O₄		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.239 (Depositor), 0.235 (DCC)
R-Value Work: 0.181 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.236	α = 90
b = 166.482	β = 90
c = 79.628	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-02-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-02-02
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2018-01-31
Changes: Experimental preparation
Version 1.4: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.5: 2024-11-13
Changes: Structure summary