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- PDB-9bs4: DNA Ligase 1 E346A/E592A double mutant with 5'-rG:C -

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Basic information

Entry
Database: PDB / ID: 9bs4
TitleDNA Ligase 1 E346A/E592A double mutant with 5'-rG:C
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
  • DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA ligase 1
  • DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
KeywordsLigase/DNA / DNA binding protein / DNA repair / BER / Human DNA Ligase 1 / LIGASE / LIGASE-DNA complex
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / 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 / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / 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) / lagging strand elongation / 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 / intracellular membrane-bounded organelle / DNA repair / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding
Similarity search - Function
: / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site ...: / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / 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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKanalElamparithi, B. / Caglayan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM14711101 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair.
Authors: Balu, K.E. / Tang, Q. / Almohdar, D. / Ratcliffe, J. / Kalaycioglu, M. / Caglayan, M.
History
DepositionMay 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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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*G)-3')
C: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
D: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
E: DNA ligase 1
F: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
G: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
H: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,87110
Polymers165,1768
Non-polymers6942
Water6,792377
1
A: DNA ligase 1
B: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
C: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
D: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9355
Polymers82,5884
Non-polymers3471
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-45 kcal/mol
Surface area31360 Å2
MethodPISA
2
E: DNA ligase 1
F: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
G: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
H: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9355
Polymers82,5884
Non-polymers3471
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-40 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.288, 117.244, 101.558
Angle α, β, γ (deg.)90.000, 96.710, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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DNA chain , 2 types, 4 molecules BFDH

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


Mass: 3405.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5446.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA/RNA hybrid , 2 types, 4 molecules AECG

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


Mass: 71581.922 Da / Num. of mol.: 2 / Mutation: E346A, E592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18858, DNA ligase (ATP)
#3: DNA/RNA hybrid DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')


Mass: 2154.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 379 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298.5 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 100mM MES pH 5.3, 18% PEG3350, 100mM Lithium acetate

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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 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 64604 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.68 Å2 / CC1/2: 0.981 / Rpim(I) all: 0.066 / Rrim(I) all: 0.173 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 1.625 / Num. unique obs: 3189 / CC1/2: 0.599 / Rpim(I) all: 0.437

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.88 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2371 2000 3.35 %
Rwork0.19 57693 -
obs0.1915 59693 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8547 1468 44 378 10437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003510438
X-RAY DIFFRACTIONf_angle_d0.595614477
X-RAY DIFFRACTIONf_chiral_restr0.03931658
X-RAY DIFFRACTIONf_plane_restr0.00411618
X-RAY DIFFRACTIONf_dihedral_angle_d20.37131933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.2946780.23162258X-RAY DIFFRACTION50.89
2.46-2.530.32451080.24773110X-RAY DIFFRACTION70.32
2.53-2.60.27591250.24753629X-RAY DIFFRACTION81.5
2.6-2.680.33781500.24564304X-RAY DIFFRACTION96.7
2.68-2.780.28651510.23744378X-RAY DIFFRACTION98.8
2.78-2.890.29391530.2364415X-RAY DIFFRACTION98.96
2.89-3.020.32021550.23154426X-RAY DIFFRACTION99.31
3.02-3.180.26031540.22154467X-RAY DIFFRACTION99.65
3.18-3.380.26711520.20614375X-RAY DIFFRACTION98.26
3.38-3.640.23591530.18154412X-RAY DIFFRACTION99.15
3.64-40.22081540.16874437X-RAY DIFFRACTION99.35
4-4.580.18911540.15324470X-RAY DIFFRACTION99.61
4.58-5.740.20821550.16254475X-RAY DIFFRACTION99.74
5.74-19.880.17671580.16434537X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: 16.7425482756 Å / Origin y: -27.0701899414 Å / Origin z: -48.4835884789 Å
111213212223313233
T0.266021885808 Å2-0.00895088520792 Å20.00920667998861 Å2-0.29849360063 Å2-0.00493313446341 Å2--0.257344773819 Å2
L0.24518247258 °2-0.046791101052 °20.00540088873224 °2-0.262588493416 °2-0.0723987406042 °2--0.149580741832 °2
S-0.018473270919 Å °0.0177782359527 Å °0.0316598875964 Å °-0.0249792777379 Å °-0.00758858445106 Å °-0.0398582893593 Å °-0.0328195328812 Å °0.0297163391351 Å °0.0286998069449 Å °
Refinement TLS groupSelection details: all

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