1FHF

THE STRUCTURE OF SOYBEAN PEROXIDASE

PDB DOI: https://doi.org/10.2210/pdb1FHF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Glycine max
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-08-01 Released: 2001-02-14
Deposition Author(s): Henriksen, A., Mirza, O., Indiana, C., Welinder, K., Teilum, K., Gajhede, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.289
R-Value Work: 0.271
R-Value Observed: 0.271

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of soybean seed coat peroxidase: a plant peroxidase with unusual stability and haem-apoprotein interactions.

Henriksen, A., Mirza, O., Indiani, C., Teilum, K., Smulevich, G., Welinder, K.G., Gajhede, M.

(2001) Protein Sci 10: 108-115

PubMed: 11266599 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1110/ps.37301
Primary Citation of Related Structures:
1FHF

PubMed Abstract:
Soybean seed coat peroxidase (SBP) is a peroxidase with extraordinary stability and catalytic properties. It belongs to the family of class III plant peroxidases that can oxidize a wide variety of organic and inorganic substrates using hydrogen peroxide. Because the plant enzyme is a heterogeneous glycoprotein, SBP was produced recombinant in Escherichia coli for the present crystallographic study. The three-dimensional structure of SBP shows a bound tris(hydroxymethyl)aminomethane molecule (TRIS). This TRIS molecule has hydrogen bonds to active site residues corresponding to the residues that interact with the small phenolic substrate ferulic acid in the horseradish peroxidase C (HRPC):ferulic acid complex. TRIS is positioned in what has been described as a secondary substrate-binding site in HRPC, and the structure of the SBP:TRIS complex indicates that this secondary substrate-binding site could be of functional importance. SBP has one of the most solvent accessible delta-meso haem edge (the site of electron transfer from reducing substrates to the enzymatic intermediates compound I and II) so far described for a plant peroxidase and structural alignment suggests that the volume of Ile74 is a factor that influences the solvent accessibility of this important site. A contact between haem C8 vinyl and the sulphur atom of Met37 is observed in the SBP structure. This interaction might affect the stability of the haem group by stabilisation/delocalisation of the porphyrin pi-cation of compound I.

Organizational Affiliation

Protein Structure Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark. [email protected]

Macromolecule Content

Total Structure Weight: 102.24 kDa
Atom Count: 7,182
Modelled Residue Count: 912
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEED COAT PEROXIDASE	A, B, C	304	Glycine max	Mutation(s): 0 EC: 1.11.1.7
UniProt
Find proteins for O22443 (Glycine max) Explore O22443 Go to UniProtKB: O22443
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O22443
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C]	F [auth A], K [auth B], P [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B]	G [auth A] H [auth A] L [auth B] M [auth B] Q [auth C] G [auth A], H [auth A], L [auth B], M [auth B], Q [auth C], R [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C]	D [auth A] E [auth A] I [auth B] J [auth B] N [auth C] D [auth A], E [auth A], I [auth B], J [auth B], N [auth C], O [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.289
R-Value Work: 0.271
R-Value Observed: 0.271
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.454	α = 90
b = 106.454	β = 90
c = 104.996	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2001-02-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-02-14
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-31
Changes: Data collection, Experimental preparation
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary