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- PDB-2l0f: Solution NMR structure of human polymerase iota UBM2 (P692A mutan... -

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Basic information

Entry
Database: PDB / ID: 2l0f
TitleSolution NMR structure of human polymerase iota UBM2 (P692A mutant) in complex with ubiquitin
Components
  • DNA polymerase iota
  • Ubiquitin
KeywordsPROTEIN BINDING / translesion DNA synthesis / DNA polymerase iota / ubiquitin-binding motif / Isopeptide bond / Nucleus / Phosphoprotein
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...: / : / protein modification process => GO:0036211 / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / 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 / translesion synthesis / error-prone translesion synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / cytosolic ribosome / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / small-subunit processome / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1630 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1630 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helix non-globular / Special / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-60S ribosomal protein L40 / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCui, G. / Benirschke, R. / Mer, G.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Basis of Ubiquitin Recognition by Translesion Synthesis DNA Polymerase iota.
Authors: Cui, G. / Benirschke, R.C. / Tuan, H.F. / Juranic, N. / Macura, S. / Botuyan, M.V. / Mer, G.
History
DepositionJul 1, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
B: DNA polymerase iota


Theoretical massNumber of molelcules
Total (without water)13,8002
Polymers13,8002
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1 / Mutation: P692A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62988, UniProt: P62979*PLUS
#2: Protein/peptide DNA polymerase iota


Mass: 5222.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNA4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HN(CA)CO
11113D H(CCO)NH
11213D C(CO)NH
11322D 1H-15N HSQC
11422D 1H-13C HSQC
11523D CBCA(CO)NH
11623D HN(CA)CB
11723D HNCO
11823D (H)CCH-TOCSY
11923D H(CCO)NH
12023D C(CO)NH
12123D 1H-15N NOESY
12223D 1H-13C NOESY
12323D 1H-15N TOCSY
12433D 15N, 13C FILTERED 13C EDITED
12543D 15N, 13C FILTERED 13C EDITED

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
25 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] UBM2, 3 mM ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O100% D2O
45 mM UBM2, 1.5 mM [U-100% 13C; U-100% 15N] ubiquitin, 20 mM sodium phosphate, 30 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 13C; U-100% 15N]1
3.5 mMentity_2-21
20 mMsodium phosphate-31
30 mMsodium chloride-41
2.5 mMentity_1-52
0.5 mMentity_2-6[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-72
30 mMsodium chloride-82
1 mMentity_1-9[U-100% 13C; U-100% 15N]3
3.5 mMentity_2-103
20 mMsodium phosphate-113
30 mMsodium chloride-123
2.5 mMentity_1-134
0.5 mMentity_2-14[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate-154
30 mMsodium chloride-164
Sample conditionsIonic strength: 0.18 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
SANEDuggan, Legge, Dyson & Wrightdata analysis
NMRView5Johnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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