3ECK | pdb_00003eck

Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations

PDB DOI: https://doi.org/10.2210/pdb3ECK/pdb

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

Deposited: 2008-08-31 Released: 2008-10-07
Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.198 (Depositor)
R-Value Work:
0.174 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Intermediate in the O-O Bond Cleavage Reaction of an Extradiol Dioxygenase.

Kovaleva, E.G., Lipscomb, J.D.

(2008) Biochemistry 47: 11168-11170

PubMed: 18826259 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi801459q
Primary Citation Related Structures:
3ECJ, 3ECK

PubMed Abstract:
The reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and O2 in adjacent ligand positions of the active site metal [usually Fe(II)]. This intermediate and the following Fe(II)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (HPCD). Here a subsequent intermediate in which the O-O bond is broken to yield a gem diol species is structurally characterized. This new intermediate is stabilized in the crystal by using the alternative substrate, 4-sulfonylcatechol, and the Glu323Leu variant of HPCD, which alters the crystal packing.

Organizational Affiliation

Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, 321 Church Street SE, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Macromolecule Content

Total Structure Weight: 168.33 kDa
Atom Count: 13,321
Modeled Residue Count: 1,436
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Homoprotocatechuate 2,3-dioxygenase)	A, B, C, D	365	Brevibacterium fuscum	Mutation(s): 1 Gene Names: hpcd EC: 1.13.11.15
UniProt
Find proteins for Q45135 (Brevibacterium fuscum) Explore Q45135 Go to UniProtKB: Q45135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q45135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XXG Query on XXG Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	N [auth C], S [auth D]	3,3-dihydroxy-4-oxocyclohexa-1,5-diene-1-sulfonic acid C₆ H₆ O₆ S JGCZOYLBGVHOFP-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain N [auth C] Focus chain S [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	G [auth A] K [auth B] O [auth C] P [auth C] T [auth D] G [auth A], K [auth B], O [auth C], P [auth C], T [auth D], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	E [auth A], H [auth B], L [auth C], Q [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	F [auth A], J [auth B], M [auth C], R [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198 (Depositor)
R-Value Work: 0.174 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.735	α = 90
b = 163.176	β = 90
c = 101.373	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Kovaleva, E.G.

Lipscomb, J.D.

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description

3ECK | pdb_00003eck

Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations

Literature

Intermediate in the O-O Bond Cleavage Reaction of an Extradiol Dioxygenase.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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