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- PDB-1fxt: STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1fxt
TitleSTRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX
Components
  • UBIQUITIN
  • UBIQUITIN-CONJUGATING ENZYME E2-24 KDA
KeywordsLIGASE / Model of the interaction between yeast Ubc1 and Ubiquitin after the formation of a covalent thiolester
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / protein modification process => GO:0036211 / vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / Peptide chain elongation / Antigen processing: Ubiquitination & Proteasome degradation ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / protein modification process => GO:0036211 / vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / Peptide chain elongation / Antigen processing: Ubiquitination & Proteasome degradation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ERAD pathway / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex
Similarity search - Function
Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. ...Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 1 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodSOLUTION NMR / Dynamic docking between Ubc1, Ub System covalently bound, minimized
AuthorsHamilton, K.S. / Shaw, G.S. / Williams, R.S. / Huzil, J.T. / McKenna, S. / Ptak, C. / Glover, M. / Ellison, M.J.
CitationJournal: Structure / Year: 2001
Title: Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail.
Authors: Hamilton, K.S. / Ellison, M.J. / Barber, K.R. / Williams, R.S. / Huzil, J.T. / McKenna, S. / Ptak, C. / Glover, M. / Shaw, G.S.
History
DepositionSep 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA
B: UBIQUITIN


Theoretical massNumber of molelcules
Total (without water)25,2742
Polymers25,2742
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)1 / 1
RepresentativeModel #1lowest energy

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Mass: 16697.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P21734, ubiquitin-protein ligase
#2: Protein UBIQUITIN


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3A-HUB / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: enhanced 1H-15N HSQC
NMR detailsText: Spectra of thiolester formation were acquired every 10 minutes during the first 60 minutes of reaction time until a stable level of covalent complex was formed

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Sample preparation

Details
Solution-IDContentsSolvent system
1Yeast Ubc10.8 mM Ubc1 10uM E1 0.8 mM Ub 10mM ATP, 5 mM MgCl, 40 mM Hepes, 450 mM NaCl,, 1 mM EDTA in water
2Human Ub0.8 mM Ubc1 10uM E1 0.8 mM Ub 10mM ATP, 5 mM MgCl, 40 mM Hepes, 450 mM NaCl,, 1 mM EDTA in water
Sample conditionsIonic strength: 450mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 30 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRDraw1Delagio and Garrettdata analysis
PIPP1Delagio and Garrettcollection
STAPP1Delagio and Garrettcollection
RefinementMethod: Dynamic docking between Ubc1, Ub System covalently bound, minimized
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 1

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