2IGA | pdb_00002iga

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

PDB DOI: https://doi.org/10.2210/pdb2IGA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brevibacterium fuscum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-09-22 Released: 2007-04-24
Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.245 (Depositor), 0.248 (DCC)
R-Value Work:
0.185 (Depositor), 0.189 (DCC)

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

Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates

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

(2007) Science 316: 453-457

PubMed: 17446402 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1134697
Primary Citation Related Structures:
2IG9, 2IGA

PubMed Abstract:
We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but not structurally characterized, in an oxygenase. The intermediates define the major chemical steps of the dioxygenase mechanism and point to a general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme family.

Organizational Affiliation

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.

Macromolecule Content

Total Structure Weight: 169.37 kDa
Atom Count: 12,927
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
Homoprotocatechuate 2,3-dioxygenase	A, B, C, D	365	Brevibacterium fuscum	Mutation(s): 0 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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XX3 Query on XX3 Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain M [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain M [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain M [auth B]	CA [auth D], M [auth B]	(1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA-3,5-DIENE C₆ H₅ N O₆ FWUJUIQFDWUIAR-LURJTMIESA-N		Interactions Focus chain CA [auth D] Focus chain M [auth B] Interactions & Density Focus chain CA [auth D] Focus chain M [auth B]
XXP Query on XXP 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-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC ACID C₆ H₅ N O₆ UDOBAQIWFWMQMT-BXTBVDPRSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
XX2 Query on XX2 Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	1-KETO,2-HYDROXY,4-NITROBENZENE, 1 ELECTRON OXIDIZED C₆ H₄ N O₄ KJBVYJMPBKCQJZ-ZCFIWIBFSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain DA [auth D]	DA [auth D] EA [auth D] H [auth A] I [auth A] N [auth B] DA [auth D], EA [auth D], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], X [auth C], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain T [auth C]	AA [auth D], E [auth A], J [auth B], T [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain J [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain J [auth B] Focus chain T [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain U [auth C] SDF format, chain F [auth A] SDF format, chain BA [auth D] MOL2 format, chain K [auth B] MOL2 format, chain U [auth C] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain K [auth B] mmCIF format, chain U [auth C] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth D]	BA [auth D], F [auth A], K [auth B], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain U [auth C]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.245 (Depositor), 0.248 (DCC)
R-Value Work: 0.185 (Depositor), 0.189 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.678	α = 90
b = 153.022	β = 90
c = 96.389	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-04-24

Deposition Author(s):

Kovaleva, E.G.

Lipscomb, J.D.

Revision History (Full details and data files)

Version 1.0: 2007-04-24
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description