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- PDB-1cqg: HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERME... -

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Basic information

Entry
Database: PDB / ID: 1cqg
TitleHIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59-71 OF THE P50 SUBUNIT OF NFKB), NMR, 31 STRUCTURES
Components
  • REF-1 PEPTIDE
  • THIOREDOXIN
KeywordsCOMPLEX (ELECTRON TRANSPORT/PEPTIDE) / COMPLEX / ELECTRON TRANSPORT/PEPTIDE / COMPLEX (ELECTRON TRANSPORT-PEPTIDE) COMPLEX
Function / homology
Function and homology information


positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / cellular detoxification of hydrogen peroxide / double-stranded DNA exodeoxyribonuclease activity ...positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / cellular detoxification of hydrogen peroxide / double-stranded DNA exodeoxyribonuclease activity / protein-disulfide reductase [NAD(P)H] activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / double-stranded telomeric DNA binding / Displacement of DNA glycosylase by APEX1 / 3'-5'-DNA exonuclease activity / positive regulation of gene expression via chromosomal CpG island demethylation / phosphoric diester hydrolase activity / thioredoxin-disulfide reductase (NADPH) activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Interconversion of nucleotide di- and triphosphates / uracil DNA N-glycosylase activity / negative regulation of protein export from nucleus / DNA catabolic process / Regulation of FOXO transcriptional activity by acetylation / phosphodiesterase I activity / positive regulation of DNA binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / Detoxification of Reactive Oxygen Species / protein-disulfide reductase activity / The NLRP3 inflammasome / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / Purinergic signaling in leishmaniasis infection / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / regulation of mRNA stability / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / TP53 Regulates Metabolic Genes / response to radiation / base-excision repair / chromatin DNA binding / RNA-DNA hybrid ribonuclease activity / transcription corepressor activity / endonuclease activity / Oxidative Stress Induced Senescence / regulation of apoptotic process / DNA recombination / damaged DNA binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear speck / ribosome / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Thioredoxin / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family ...AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Thioredoxin / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin / DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, G.M. / Qin, J. / Gronenborn, A.M.
Citation
Journal: Structure / Year: 1996
Title: The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal.
Authors: Qin, J. / Clore, G.M. / Kennedy, W.P. / Kuszewski, J. / Gronenborn, A.M.
#1: Journal: Structure / Year: 1995
Title: Solution Structure of Human Thioredoxin in a Mixed Disulfide Intermediate Complex with its Target Peptide from the Transcription Factor NF Kappa B
Authors: Qin, J. / Clore, G.M. / Kennedy, W.M. / Huth, J.R. / Gronenborn, A.M.
#2: Journal: Structure / Year: 1994
Title: The High-Resolution Three-Dimensional Solution Structures of the Oxidized and Reduced States of Human Thioredoxin
Authors: Qin, J. / Clore, G.M. / Gronenborn, A.M.
#3: Journal: Biochemistry / Year: 1991
Title: High-Resolution Three-Dimensional Structure of Reduced Recombinant Human Thioredoxin in Solution
Authors: Forman-Kay, J.D. / Clore, G.M. / Wingfield, P.T. / Gronenborn, A.M.
History
DepositionApr 2, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type / _pdbx_database_related.details / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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

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Assembly

Deposited unit
A: THIOREDOXIN
B: REF-1 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,9972
Polymers12,9972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / -
Representative

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Components

#1: Protein THIOREDOXIN


Mass: 11592.125 Da / Num. of mol.: 1 / Mutation: CHAIN A, C35A, C62A, C69A, C73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / References: UniProt: P10599
#2: Protein/peptide REF-1 PEPTIDE


Mass: 1404.611 Da / Num. of mol.: 1 / Fragment: RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB
Source method: isolated from a genetically manipulated source
References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase
Has protein modificationY
Sequence detailsTHR AT POSITION 74 WAS FOUND BY WOLMAN ET AL., JOURNAL OF BIOCHEMISTRY 263, 15506 (1988).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementSoftware ordinal: 1
Details: OTHER REFINEMENT REMARKS: THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & ...Details: OTHER REFINEMENT REMARKS: THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324. MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1994) J. MAGN. RESON SERIES B 104 99 - 103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96), AND PROTON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON SERIES B 107, 293 - 297) RESTRAINTS, AND A CONFORMATIONAL DATABASE POTENTIAL TERM (KUSZEWSKI, GRONENBORN & CLORE (1996) PROTEIN SCIENCE IN PRESS). ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE. THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL RESTRAINTS COMPRISING: 2581 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS 36 RESTRAINTS FOR 18 BACKBONE H-BONDS 321 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1, AND 30 CHI2 FOR HUMAN THIOREDOXIN, AND 11 PHI, 9 PSI, 9 CHI1, AND 4 CHI2 ANGLES FOR THE REF-1 PEPTIDE 86 HN-HALPHA THREE-BOND COUPLING CONSTANTS 100 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS. 442 1H CHEMICAL SHIFT RESTRAINTS (MADE UP OF 113 CAH, 67 METHYL GROUPS AND 262 OTHER NON-EXCHANGEABLE PROTONS). THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS FOLLOWS: INTRAMOLECULAR HTRX RESTRAINTS: 534 SEQUENTIAL 539 SHORT RANGE (1 < |I-J|<=5) 688 LONG RANGE (|I-J|>5) 682 INTRARESIDUE INTRAMOLECULAR PEPTIDE RESTRAINTS: 83 INTERMOLECULAR HTRX-NFKB: 55 THE STRUCTURE FOUND IN PDB ENTRY 1CQH IS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 35 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 1 - 105 OF HTRX AND RESIDUES 57 - 67 OF THE PEPTIDE AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE LAST NUMBER COLUMN IN THIS SET OF COORDINATES (THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE.
NMR ensembleConformers submitted total number: 35

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