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- PDB-6p0e: Human DNA Ligase 1 (E346A,E592A) bound to adenylated DNA containi... -

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Basic information

Entry
Database: PDB / ID: 6p0e
TitleHuman DNA Ligase 1 (E346A,E592A) bound to adenylated DNA containing an 8-oxo guanine:adenine base-pair
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(8OG))-3')
  • DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*AP*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 / protein-DNA complex / phosphotransferase / OB fold / DNA Binding domain / Adenylation Domain / metalloenzyme
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
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
DepositionMay 16, 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*(8OG))-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*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3988
Polymers82,7004
Non-polymers6984
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-34 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.676, 100.939, 115.360
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: 71669.938 Da / Num. of mol.: 1 / Fragment: residues 262-904 / Mutation: E346A, E592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Production host: Escherichia coli (E. coli) / 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*(8OG))-3')


Mass: 3421.220 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*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5470.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 733 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350

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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: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 71710 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 31.92 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.041 / Rrim(I) all: 0.112 / Χ2: 1.002 / Net I/σ(I): 7.8 / Num. measured all: 534920
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.926.41.40670980.5430.5921.5290.951100
1.92-1.997.51.06170940.7390.4131.1390.998100
1.99-2.087.60.70770520.8620.2730.7581.021100
2.08-2.197.60.4971180.9270.1890.5251.016100
2.19-2.337.60.3370940.9650.1270.3541.024100
2.33-2.517.70.22871370.9810.0880.2450.998100
2.51-2.767.70.15271560.990.0590.1631.004100
2.76-3.167.60.09871830.9950.0380.1051.015100
3.16-3.997.60.06972570.9980.0270.0740.992100
3.99-507.30.06775210.9950.0260.0720.99699.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x9n

1x9n


Resolution: 1.85→41.266 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.94
RfactorNum. reflection% reflection
Rfree0.1838 3606 5.04 %
Rwork0.1546 --
obs0.1562 71615 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.5 Å2 / Biso mean: 44.4857 Å2 / Biso min: 13.37 Å2
Refinement stepCycle: final / Resolution: 1.85→41.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 736 91 735 6576
Biso mean--49.99 47.27 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066140
X-RAY DIFFRACTIONf_angle_d0.8588505
X-RAY DIFFRACTIONf_chiral_restr0.048955
X-RAY DIFFRACTIONf_plane_restr0.005972
X-RAY DIFFRACTIONf_dihedral_angle_d16.7313652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8492-1.87360.31051170.27322107222480
1.8736-1.89920.25651400.261225802720100
1.8992-1.92640.2781360.247626102746100
1.9264-1.95510.26371350.229425942729100
1.9551-1.98570.27011360.224626142750100
1.9857-2.01820.23771380.215626232761100
2.0182-2.0530.19981380.195225742712100
2.053-2.09040.23621390.188626182757100
2.0904-2.13060.19571420.183326142756100
2.1306-2.17410.20011370.179126222759100
2.1741-2.22130.1951250.173226252750100
2.2213-2.2730.23531160.170126112727100
2.273-2.32980.17631220.167226452767100
2.3298-2.39280.20391440.152726312775100
2.3928-2.46320.18161610.157826072768100
2.4632-2.54270.19391450.156126022747100
2.5427-2.63360.19771350.156626292764100
2.6336-2.7390.19611270.159526642791100
2.739-2.86360.21811450.161326372782100
2.8636-3.01460.22371510.171726302781100
3.0146-3.20340.18261410.162826282769100
3.2034-3.45060.19161360.14262659279599
3.4506-3.79760.14151450.1426492794100
3.7976-4.34660.14861450.119426892834100
4.3466-5.47430.15811680.1227042872100
5.4743-41.27620.17081420.150228432985100
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)
11.30520.0844-0.0940.8484-0.04481.16140.0578-0.06640.25140.0702-0.025-0.0109-0.15420.0173-0.00010.2431-0.00830.01390.2294-0.02130.283533.300412.0373-11.3204
20.5050.0504-0.62980.1278-0.10460.79960.2119-0.35580.17740.5577-0.1475-0.1637-0.35210.3956-0.00470.4426-0.08720.02150.3551-0.03670.314637.166211.2562.6319
30.72570.4897-0.0831.07780.00870.8996-0.0450.0315-0.0146-0.0334-0.0077-0.1240.09270.099200.21480.00950.02210.25820.01640.267936.58750.4592-18.1907
41.2401-0.0644-0.75671.32980.92461.2907-0.03480.0697-0.0551-0.04160.00150.0075-0.0074-0.049400.23420.01620.02550.1811-0.00280.220618.9345-21.4187-16.0513
51.0384-0.2727-0.06371.1090.35760.6008-0.0743-0.0531-0.15320.07380.05590.05840.19-0.044300.26420.01610.0420.20490.01820.257417.4123-24.6922-10.4646
60.8715-0.8190.33851.36650.46321.1819-0.02540.1725-0.2037-0.2099-0.09710.19350.0299-0.2616-0.00130.2869-0.01140.00030.3209-0.03310.289710.6232-22.087-23.1858
72.1712-0.4434-0.96011.66760.82381.51320.09650.06230.23840.0559-0.10520.2659-0.0792-0.20610.00030.23770.04920.01810.25310.01260.3119-1.22855.6881-7.3585
81.56170.1035-0.4721.34320.520.6138-0.0750.03660.01770.14490.10550.35760.107-0.3388-00.26890.02780.03410.31860.02930.3339-6.4996-3.7726-5.0943
90.06950.10210.09530.14960.13960.13010.2717-0.0991-0.02240.14020.2033-0.2981-0.371-0.25640.02880.41590.03070.02910.4076-0.04810.258416.8518-4.07189.0297
10-0.0001-0.0034-0.00630.14250.26510.4927-0.07240.20380.1385-0.01760.19520.12320.08380.1350.00020.26480.01810.00510.30950.03120.276211.92792.9054-21.1163
110.5276-0.156-0.20940.6188-0.23610.23740.02960.0210.1451-0.00950.13850.14440.1440.02520.00030.25880.00760.01050.2499-0.00640.258814.40110.7749-15.0937
122.14120.41940.96080.18560.26570.4882-0.0143-0.1042-0.2769-0.05640.4381-0.1246-0.48140.1990.35180.49060.04040.01260.3732-0.02710.241918.9239-4.470312.0093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 260 through 385 )A260 - 385
2X-RAY DIFFRACTION2chain 'A' and (resid 386 through 418 )A386 - 418
3X-RAY DIFFRACTION3chain 'A' and (resid 419 through 544 )A419 - 544
4X-RAY DIFFRACTION4chain 'A' and (resid 545 through 624 )A545 - 624
5X-RAY DIFFRACTION5chain 'A' and (resid 625 through 685 )A625 - 685
6X-RAY DIFFRACTION6chain 'A' and (resid 686 through 741 )A686 - 741
7X-RAY DIFFRACTION7chain 'A' and (resid 742 through 852 )A742 - 852
8X-RAY DIFFRACTION8chain 'A' and (resid 853 through 901 )A853 - 901
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 12 )B3 - 12
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 7 )C1 - 7
11X-RAY DIFFRACTION11chain 'D' and (resid 9 through 18 )D9 - 18
12X-RAY DIFFRACTION12chain 'D' and (resid 19 through 26 )D19 - 26

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