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- PDB-6q1v: Human DNA Ligase 1 (E592R) Bound to an Adenylated, hydroxyl termi... -

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Basic information

Entry
Database: PDB / ID: 6q1v
TitleHuman DNA Ligase 1 (E592R) Bound to an Adenylated, hydroxyl terminated DNA nick
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
  • DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
  • DNA ligase 1
KeywordsLIGASE/DNA / protein-DNA complex / phosphotransferase / OB fold / DNA Binding domain / Adenylation Domain / metalloenzyme / LIGASE / LIGASE-DNA complex
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / lagging strand elongation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / lagging strand elongation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA biosynthetic process / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mismatch repair / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA recombination / cell division / DNA repair / intracellular membrane-bounded organelle / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase AMP-binding site. ...DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchellenberg, M.J. / Williams, R.S. / Tumbale, P.S. / Riccio, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nat Commun / Year: 2019
Title: Two-tiered enforcement of high-fidelity DNA ligation.
Authors: Tumbale, P.P. / Jurkiw, T.J. / Schellenberg, M.J. / Riccio, A.A. / O'Brien, P.J. / Williams, R.S.
History
DepositionAug 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase 1
B: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
C: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
D: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4398
Polymers82,8044
Non-polymers6354
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-43 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.486, 101.171, 115.291
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA ligase 1 / DNA ligase I / Polydeoxyribonucleotide synthase [ATP] 1


Mass: 71814.102 Da / Num. of mol.: 1 / Mutation: E592R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18858, DNA ligase (ATP)

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DNA chain , 3 types, 3 molecules BCD

#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')


Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5486.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 466 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.841→50 Å / Num. obs: 72997 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Rrim(I) all: 0.084 / Χ2: 1.006 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.85-1.92771980.5630.6060.919100
1.92-1.99772000.7380.3990.9831000.98
1.99-2.08772100.8610.2561.0231000.6310.681
2.08-2.197.172560.9270.171.0331000.420.454
2.19-2.337.172360.9660.1161.0311000.2880.311
2.33-2.517.172680.980.0831.0381000.2040.221
2.51-2.76773090.9890.0570.9931000.140.151
2.76-3.166.973020.9930.041.01799.80.0970.105
3.16-3.996.673770.9960.0291.00399.80.0680.074
3.99-506.676410.9970.0221.01999.60.0540.058

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x9n

1x9n


Resolution: 1.85→38.875 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.65
RfactorNum. reflection% reflection
Rfree0.1936 3661 5.02 %
Rwork0.1625 --
obs0.1641 72890 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.49 Å2 / Biso mean: 48.2933 Å2 / Biso min: 22.19 Å2
Refinement stepCycle: final / Resolution: 1.85→38.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 733 68 466 6291
Biso mean--64.1 48.29 -
Num. residues----678
LS refinement shellResolution: 1.85→1.8648 Å
RfactorNum. reflection
Rfree0.3127 -
Rwork0.2728 -
obs-2620
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0585-0.078-0.43371.542-0.29441.89430.083-0.19360.30450.1827-0.02010.0468-0.2939-0.025-0.07860.3198-0.02060.00530.2607-0.02410.347833.57913.109-9.594
21.07150.3847-0.3881.3524-0.42571.4056-0.05330.0103-0.0089-0.0261-0.0312-0.14990.05180.10670.07460.2117-0.003-0.00390.24760.01580.299836.3350.545-15.774
31.8607-0.5393-0.29661.84460.56442.2004-0.04670.0971-0.0968-0.0480.0130.11920.0118-0.19660.03570.2649-0.00280.01580.2297-0.00970.277716.076-22.574-16.276
42.4931-0.332-0.86372.290.30491.75650.05250.01140.1760.0781-0.02850.3078-0.1122-0.2460.00030.24980.0375-0.00150.31930.00850.3003-3.122.614-6.632
50.48980.06681.55940.32890.10085.64480.3136-0.1708-0.0020.28470.1925-0.2199-0.3438-0.2749-0.48890.4009-0.02010.0130.4052-0.01860.301316.235-4.7417.295
63.33751.4478-1.70121.6688-1.08394.30360.00870.20020.2797-0.04920.19850.20840.23040.0778-0.18140.35380.02380.00680.35440.0120.328611.6272.885-21.198
71.99030.6646-1.88760.8157-0.76942.8786-0.01480.01020.0522-0.13580.13760.07220.13310.1472-0.10230.3650.00860.00110.3365-0.01470.328714.1310.73-15.138
81.89420.88131.43212.04792.35425.05310.06550.05230.0447-0.04670.2122-0.0149-0.5240.0977-0.24150.42370.01840.02570.40720.03210.304818.559-4.6111.952
92.2172-0.0798-1.15535.57214.4434.09710.04370.2469-0.1076-0.8997-0.3277-0.0875-0.63270.05430.16810.94840.1981-0.00460.686-0.02370.585213.349-15.686-17.082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A260 - 400
2X-RAY DIFFRACTION2A401 - 544
3X-RAY DIFFRACTION3A545 - 741
4X-RAY DIFFRACTION4A742 - 901
5X-RAY DIFFRACTION5B3 - 13
6X-RAY DIFFRACTION6C1 - 7
7X-RAY DIFFRACTION7D9 - 18
8X-RAY DIFFRACTION8D19 - 26
9X-RAY DIFFRACTION9C101

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