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

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Basic information

Entry
Database: PDB / ID: 4yoq
TitleCrystal Structure of 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 glycosylase / adenine/guanine mispair binding / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine 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 / DNA glycosylase / Endonuclease III; domain 1 / 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: 2.21 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 11, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,2896
Polymers48,8223
Non-polymers4673
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-51 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.697, 84.594, 142.457
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 A/G-specific adenine glycosylase


Mass: 42098.926 Da / Num. of mol.: 1 / Mutation: N144D, 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

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DNA chain , 2 types, 2 molecules BC

#2: 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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')


Mass: 3300.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 130 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, pH 8.0, 250 mM NaOAc, 29% (wt/vol) PEG 4000

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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: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.21→142.46 Å / Num. obs: 23671 / % possible obs: 99.9 % / Redundancy: 6.9 % / Net I/σ(I): 11.3
Reflection shellResolution: 2.21→2.28 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.523 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RRQ

1rrq


Resolution: 2.21→41.408 Å / FOM work R set: 0.8014 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 1216 5.15 %
Rwork0.1844 22392 -
obs0.1876 23608 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.8 Å2 / Biso mean: 57.62 Å2 / Biso min: 15.85 Å2
Refinement stepCycle: final / Resolution: 2.21→41.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 426 15 127 3333
Biso mean--54.7 48.35 -
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013327
X-RAY DIFFRACTIONf_angle_d1.3994609
X-RAY DIFFRACTIONf_chiral_restr0.081498
X-RAY DIFFRACTIONf_plane_restr0.006523
X-RAY DIFFRACTIONf_dihedral_angle_d19.6171264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.21-2.29850.38211400.30223972537
2.2985-2.40310.32961390.268624352574
2.4031-2.52980.28611420.231624602602
2.5298-2.68830.29371260.222224722598
2.6883-2.89580.29411430.206924602603
2.8958-3.18710.25231180.196424892607
3.1871-3.6480.24861290.168224792608
3.648-4.59520.2121370.149525312668
4.5952-41.41520.21821420.167926692811
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)
11.91360.5771-0.61263.8510.9033.80020.091.24380.0522-0.6275-0.19560.47470.26220.00470.10250.3210.074-0.06930.62370.04310.3736.14987.68840.5544
21.88260.68260.14825.9826-1.11843.647-0.12730.01320.96370.4310.00790.225-0.64830.11880.0260.299-0.0143-0.0120.22080.05910.468213.038199.974215.8475
33.48280.5970.31494.63861.16691.8504-0.0691.3679-0.3653-0.56440.1125-0.4178-0.16340.2119-0.01340.3138-0.03130.04440.7226-0.03010.301416.070884.4421-1.6293
40.11060.2655-0.30023.3222.5084.684-0.28210.6935-0.8373-0.08370.0002-0.12310.2617-0.179-1.15650.44920.02020.01970.825-0.67010.984615.290567.21020.0077
52.77910.164-0.05312.5802-0.46294.53190.0701-1.03970.53821.12490.1752-0.49710.03110.5439-0.13230.742-0.018-0.13740.6929-0.12790.428220.985392.91539.1431
65.474-5.548-5.79785.61835.86596.1272-0.5965-0.405-0.76040.34190.3905-1.0370.82940.99050.19850.34410.01750.06180.50160.00690.668430.900483.063214.6483
71.2473-1.6701-1.65543.83261.1462.9126-0.04710.0909-1.7956-0.2216-0.13180.83511.2902-1.0760.2460.8297-0.2317-0.0430.44640.04270.90859.472977.782121.2065
87.0919-0.0289-0.69393.44980.62286.0626-0.0074-0.6456-0.77720.2828-0.227-0.45251.36430.39370.21520.51060.07-0.02650.58130.13780.517520.72780.650813.6076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:50 )A9 - 50
2X-RAY DIFFRACTION2( CHAIN A AND RESID 51:105 )A51 - 105
3X-RAY DIFFRACTION3( CHAIN A AND RESID 106:210 )A106 - 210
4X-RAY DIFFRACTION4( CHAIN A AND RESID 211:234 )A211 - 234
5X-RAY DIFFRACTION5( CHAIN A AND RESID 235:360 )A235 - 360
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:5 )B1 - 5
7X-RAY DIFFRACTION7( CHAIN B AND RESID 7:11 )B7 - 11
8X-RAY DIFFRACTION8( CHAIN C AND RESID 13:22 )C13 - 22

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