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- PDB-4ypr: Crystal Structure of D144N MutY bound to its anti-substrate -

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Basic information

Entry
Database: PDB / ID: 4ypr
TitleCrystal Structure of D144N MutY bound to its anti-substrate
Components
  • A/G-specific adenine glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')
KeywordsHydrolase/DNA / 8-oxoguanine / base-excision repair / anti-substrate / Hydrolase-DNA complex
Function / homology
Function and homology information


adenine/guanine mispair binding / adenine glycosylase / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) ...A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsWang, L. / Lee, S. / Verdine, G.L.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.
Authors: Wang, L. / Lee, S.J. / Verdine, G.L.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A/G-specific adenine glycosylase
B: A/G-specific adenine glycosylase
C: DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
E: DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')
F: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3468
Polymers97,6436
Non-polymers7032
Water52229
1
A: A/G-specific adenine glycosylase
C: DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1734
Polymers48,8213
Non-polymers3521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-36 kcal/mol
Surface area18320 Å2
MethodPISA
2
B: A/G-specific adenine glycosylase
E: DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')
F: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1734
Polymers48,8213
Non-polymers3521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-41 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.272, 105.272, 235.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein A/G-specific adenine glycosylase


Mass: 42097.941 Da / Num. of mol.: 2 / Mutation: P164C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P83847, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: DNA chain DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')


Mass: 3300.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')


Mass: 3423.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 100 mM Tris, pH 8.6, 1.75 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.59→117.69 Å / Num. obs: 45851 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 50.22 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.054 / Net I/σ(I): 15.5 / Num. measured all: 262741
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALA0.1.27data scaling
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RRQ

1rrq


Resolution: 2.59→85.014 Å / FOM work R set: 0.818 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 2310 5.05 %
Rwork0.1694 43456 -
obs0.1724 45766 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.01 Å2 / Biso mean: 57.65 Å2 / Biso min: 23.66 Å2
Refinement stepCycle: final / Resolution: 2.59→85.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5678 852 16 29 6575
Biso mean--38.21 44.61 -
Num. residues----747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126798
X-RAY DIFFRACTIONf_angle_d1.4469417
X-RAY DIFFRACTIONf_chiral_restr0.0591013
X-RAY DIFFRACTIONf_plane_restr0.0071077
X-RAY DIFFRACTIONf_dihedral_angle_d21.2542589
LS refinement shellResolution: 2.59→2.6463 Å
RfactorNum. reflection% reflection
Rfree0.3621 139 -
Rwork0.2921 2711 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 32.934 Å / Origin y: 41.7401 Å / Origin z: -7.7291 Å
111213212223313233
T0.4924 Å2-0.085 Å2-0.045 Å2-0.3869 Å2-0 Å2--0.2868 Å2
L0.4502 °20.8377 °20.2714 °2-1.4499 °20.6437 °2---0.0777 °2
S0.0074 Å °0.0292 Å °-0.0689 Å °0.0986 Å °0.0375 Å °-0.0825 Å °0.0251 Å °-0.0036 Å °-0.0544 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 400
2X-RAY DIFFRACTION1allB6 - 400
3X-RAY DIFFRACTION1allC13 - 22
4X-RAY DIFFRACTION1allD1 - 11
5X-RAY DIFFRACTION1allE13 - 22
6X-RAY DIFFRACTION1allF1 - 11
7X-RAY DIFFRACTION1allG1 - 29

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