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- PDB-5f6y: Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment... -

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Basic information

Entry
Database: PDB / ID: 5f6y
TitleCrystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)
ComponentsSUMO-conjugating enzyme UBC9
KeywordsLIGASE/LIGASE inhibitor / Ubc9 / Fragment drug design / sumoylation / LIGASE-LIGASE inhibitor complex
Function / homology
Function and homology information


SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly ...SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / nuclear export / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / postsynaptic cytosol / nuclear pore / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / Meiotic synapsis / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / PML body / PKR-mediated signaling / modulation of chemical synaptic transmission / protein modification process / Schaffer collateral - CA1 synapse / Formation of Incision Complex in GG-NER / nuclear envelope / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
5-chloranyl-3~{H}-1,3-benzoxazole-2-thione / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsLountos, G.T. / Hewitt, W.M. / Zlotkowski, K. / Dahlhauser, S. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. ...Lountos, G.T. / Hewitt, W.M. / Zlotkowski, K. / Dahlhauser, S. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. / Nussinov, R. / Schneekloth, J.S.Jr. / Waugh, D.S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.
Authors: Hewitt, W.M. / Lountos, G.T. / Zlotkowski, K. / Dahlhauser, S.D. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. / Nussinov, R. / Waugh, D.S. / Schneekloth, J.S.
History
DepositionDec 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 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 / 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 / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9112
Polymers17,7251
Non-polymers1861
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.237, 35.492, 58.122
Angle α, β, γ (deg.)90.00, 111.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUMO-conjugating enzyme UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin- ...SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / p18


Mass: 17725.375 Da / Num. of mol.: 1 / Mutation: K48A,K49A,E54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: pDN2405 / Production host: Escherichia coli (E. coli)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-5VM / 5-chloranyl-3~{H}-1,3-benzoxazole-2-thione


Mass: 185.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4ClNOS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→50 Å / Num. obs: 65740 / % possible obs: 94.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.8
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9B

1u9b


Resolution: 1.14→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.978 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17777 3311 5 %RANDOM
Rwork0.15559 ---
obs0.1567 62405 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.64 Å2
2---0.41 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 11 185 1437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221440
X-RAY DIFFRACTIONr_bond_other_d0.0070.021048
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9891989
X-RAY DIFFRACTIONr_angle_other_deg0.94632578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31523.78866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30115259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2311511
X-RAY DIFFRACTIONr_chiral_restr0.1190.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8651.5859
X-RAY DIFFRACTIONr_mcbond_other0.5361.5328
X-RAY DIFFRACTIONr_mcangle_it2.8821420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8853581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8054.5549
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.56932488
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 170 -
Rwork0.202 3382 -
obs--69.78 %

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