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- PDB-2rm5: Glutathione peroxidase-type tryparedoxin peroxidase, oxidized form -

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Basic information

Entry
Database: PDB / ID: 2rm5
TitleGlutathione peroxidase-type tryparedoxin peroxidase, oxidized form
ComponentsGlutathione peroxidase-like protein
KeywordsOXIDOREDUCTASE / tryparedoxin / peroxidase / oxidized
Function / homology
Function and homology information


glycosome / peroxidase activity / response to oxidative stress
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione peroxidase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsMelchers, J. / Feher, K. / Diechtierow, M. / Krauth-Siegel, L. / Tews, I. / Muhle-Goll, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for a distinct catalytic mechanism in Trypanosoma brucei tryparedoxin peroxidase
Authors: Melchers, J. / Diechtierow, M. / Feher, K. / Sinning, I. / Tews, I. / Krauth-Siegel, R.L. / Muhle-Goll, C.
History
DepositionOct 3, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione peroxidase-like protein


Theoretical massNumber of molelcules
Total (without water)18,6031
Polymers18,6031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Glutathione peroxidase-like protein / Trypanothione/tryparedoxin dependent peroxidase 3


Mass: 18603.244 Da / Num. of mol.: 1 / Fragment: residues 10-176 / Mutation: C76S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: gpx3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q869A5, glutathione peroxidase
Has protein modificationY
Sequence detailsTHE AUTHOR STATES THAT THE SEQUENCE DIFFERS FROM THE SEQUENCE DEPOSITED IN THE NCBI BECAUSE OF ...THE AUTHOR STATES THAT THE SEQUENCE DIFFERS FROM THE SEQUENCE DEPOSITED IN THE NCBI BECAUSE OF MICRO HETEROGENICITY IN THE PEROXIDASE GENE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-1H NOESY
1223D 1H-13C NOESY
1313D 1H-15N NOESY
1413D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM [U-100% 15N] tryparedoxin peroxidase; 90% H2O/10% D2O90% H2O/10% D2O
21.2mM [U-100% 13C; U-100% 15N] tryparedoxin peroxidase; 100% D2O100% D2O
31.2 mM tryparedoxin peroxidase; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMtryparedoxin peroxidase[U-100% 15N]1
1.2 mMtryparedoxin peroxidase[U-100% 13C; U-100% 15N]2
1.2 mMtryparedoxin peroxidase3
Sample conditionsIonic strength: 150 / pH: 6.8 / Pressure: ambient / Temperature: 297 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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