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- PDB-5jcg: Structure of Human Peroxiredoxin 3 as three stacked rings -

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Basic information

Entry
Database: PDB / ID: 5jcg
TitleStructure of Human Peroxiredoxin 3 as three stacked rings
ComponentsThioredoxin-dependent peroxide reductase, mitochondrial
KeywordsOXIDOREDUCTASE / Peroxidase / molecular chaperone / peroxiredoxin
Function / homology
Function and homology information


NADH-dependent peroxiredoxin activity / negative regulation of kinase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Detoxification of Reactive Oxygen Species / cell redox homeostasis / regulation of mitochondrial membrane potential ...NADH-dependent peroxiredoxin activity / negative regulation of kinase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Detoxification of Reactive Oxygen Species / cell redox homeostasis / regulation of mitochondrial membrane potential / cellular response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrion organization / response to hydrogen peroxide / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / response to oxidative stress / response to lipopolysaccharide / early endosome / mitochondrial matrix / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / protein kinase binding / negative regulation of apoptotic process / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...: / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-dependent peroxide reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYewdall, N.A. / Gerrard, J.A. / Goldstone, D.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
RSNZRDF-UOA-1303 New Zealand
CitationJournal: Structure / Year: 2016
Title: Structures of Human Peroxiredoxin 3 Suggest Self-Chaperoning Assembly that Maintains Catalytic State.
Authors: N Amy Yewdall / Hariprasad Venugopal / Ambroise Desfosses / Vahid Abrishami / Yuliana Yosaatmadja / Mark B Hampton / Juliet A Gerrard / David C Goldstone / Alok K Mitra / Mazdak Radjainia /
Abstract: Peroxiredoxins are antioxidant proteins primarily responsible for detoxification of hydroperoxides in cells. On exposure to various cellular stresses, peroxiredoxins can acquire chaperone activity, ...Peroxiredoxins are antioxidant proteins primarily responsible for detoxification of hydroperoxides in cells. On exposure to various cellular stresses, peroxiredoxins can acquire chaperone activity, manifested as quaternary reorganization into a high molecular weight (HMW) form. Acidification, for example, causes dodecameric rings of human peroxiredoxin 3 (HsPrx3) to stack into long helical filaments. In this work, a 4.1-Å resolution structure of low-pH-instigated helical filaments was elucidated, showing a locally unfolded active site and partially folded C terminus. A 2.8-Å crystal structure of HsPrx3 was determined at pH 8.5 under reducing conditions, wherein dodecameric rings are arranged as a short stack, with symmetry similar to low-pH filaments. In contrast to previous observations, the crystal structure displays both a fully folded active site and ordered C terminus, suggesting that the HsPrx3 HMW form maintains catalytic activity. We propose a new role for the HMW form as a self-chaperoning assembly maintaining HsPrx3 function under stress.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-dependent peroxide reductase, mitochondrial
B: Thioredoxin-dependent peroxide reductase, mitochondrial
C: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
E: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)199,7479
Polymers199,7479
Non-polymers00
Water2,864159
1
A: Thioredoxin-dependent peroxide reductase, mitochondrial
B: Thioredoxin-dependent peroxide reductase, mitochondrial
C: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
E: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial

A: Thioredoxin-dependent peroxide reductase, mitochondrial
B: Thioredoxin-dependent peroxide reductase, mitochondrial
C: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
E: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial

A: Thioredoxin-dependent peroxide reductase, mitochondrial
B: Thioredoxin-dependent peroxide reductase, mitochondrial
C: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
E: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial

A: Thioredoxin-dependent peroxide reductase, mitochondrial
B: Thioredoxin-dependent peroxide reductase, mitochondrial
C: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
E: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)798,99036
Polymers798,99036
Non-polymers00
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_544x,-y-1,-z-11
Unit cell
Length a, b, c (Å)133.188, 168.730, 221.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Thioredoxin-dependent peroxide reductase, mitochondrial / Antioxidant protein 1 / AOP-1 / HBC189 / Peroxiredoxin III / Prx-III / Peroxiredoxin-3 / Protein MER5 homolog


Mass: 22194.162 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX3, AOP1 / Plasmid: pET151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P30048, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5% PEG1000, 12.5% PEG3350. 12.5% MPD, 0.02 M alcohol additives at pH 8.5 (Gorrec, 2009)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→52.27 Å / Num. obs: 61455 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.954 / Rmerge(I) obs: 0.176 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.713 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYE

1zye


Resolution: 2.8→52.27 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.847 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.085 / ESU R Free: 0.317
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 3005 4.9 %RANDOM
Rwork0.1826 ---
obs0.1849 58445 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.58 Å2 / Biso mean: 22.738 Å2 / Biso min: 4.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å2-0 Å2
2--1.8 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.8→52.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13658 0 0 159 13817
Biso mean---15.16 -
Num. residues----1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914027
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213188
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.95119118
X-RAY DIFFRACTIONr_angle_other_deg0.939330399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38951746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21924.466618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.124152180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7711545
X-RAY DIFFRACTIONr_chiral_restr0.0790.22160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023231
X-RAY DIFFRACTIONr_mcbond_it0.8972.2567011
X-RAY DIFFRACTIONr_mcbond_other0.8972.2567010
X-RAY DIFFRACTIONr_mcangle_it1.5873.3818748
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 198 -
Rwork0.299 4285 -
all-4483 -
obs--99.58 %

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