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Basic information

Entry
Database: PDB / ID: 3n5n
TitleCrystal structure analysis of the catalytic domain and interdomain connector of human MutY homologue
ComponentsA/G-specific adenine DNA glycosylase
KeywordsHYDROLASE / alpha-helices / helix-hairpin-helix motif / iron-sulfur cluster
Function / homology
Function and homology information


Defective MUTYH substrate binding / Defective MUTYH substrate processing / adenine/guanine mispair binding / adenine glycosylase / depurination / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 ...Defective MUTYH substrate binding / Defective MUTYH substrate processing / adenine/guanine mispair binding / adenine glycosylase / depurination / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / negative regulation of necroptotic process / oxidized purine DNA binding / mismatch repair / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA repair / mitochondrion / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES ...Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / 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 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / IRON/SULFUR CLUSTER / Adenine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, Molecular Replacement / Resolution: 2.3 Å
AuthorsToth, E.A. / Luncsford, P.J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A structural hinge in eukaryotic MutY homologues mediates catalytic activity and Rad9-Rad1-Hus1 checkpoint complex interactions.
Authors: Luncsford, P.J. / Chang, D.Y. / Shi, G. / Bernstein, J. / Madabushi, A. / Patterson, D.N. / Lu, A.L. / Toth, E.A.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: A/G-specific adenine DNA glycosylase
Y: A/G-specific adenine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2725
Polymers63,5102
Non-polymers7623
Water99155
1
X: A/G-specific adenine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1062
Polymers31,7551
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
Y: A/G-specific adenine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1663
Polymers31,7551
Non-polymers4112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.311, 82.167, 63.460
Angle α, β, γ (deg.)90.00, 100.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21Y
12X
22Y
13X
23Y

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU2XA68 - 3094 - 245
21SERSERLEULEU2YB68 - 3094 - 245
12SF4SF4SF4SF41XC400
22SF4SF4SF4SF41YD400
13VALVALASNASN4XA315 - 343251 - 279
23VALVALASNASN4YB315 - 343251 - 279

NCS ensembles :
ID
1
2
3

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Components

#1: Protein A/G-specific adenine DNA glycosylase / MutY homolog / hMYH


Mass: 31754.820 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP residues 76-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUTYH, MYH / Plasmid: pET19b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 DE3
References: UniProt: Q9UIF7, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 49.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 20% PEG 3350, 0.2M Magnesium acetate, 0.005 M tris[2-carboxyethyl] phosphine (TCEP), 5% glycerol, 0.01 M spermidine, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.65 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2007
Details: Si(111) channel-cut monochromator, toroidal focusing mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65 Å / Relative weight: 1
ReflectionResolution: 2.3→62.31 Å / Num. all: 27002 / Num. obs: 25872 / % possible obs: 95.8 % / Redundancy: 7.6 % / Rsym value: 0.097 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.437 / % possible all: 93.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREplus Molrepphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD, Molecular Replacement
Starting model: PDB Entry 1MUY

1muy


Resolution: 2.3→62.31 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.561 / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.243
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.25078 1302 5 %RANDOM
Rwork0.20616 ---
obs0.20843 24674 95.66 %-
all-27002 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.249 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å2-2.6 Å2
2---5.43 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4037 0 19 55 4111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9595670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.25723.714175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36315611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0921534
X-RAY DIFFRACTIONr_chiral_restr0.1590.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213182
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4591.52698
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.83524274
X-RAY DIFFRACTIONr_scbond_it6.32831447
X-RAY DIFFRACTIONr_scangle_it9.1154.51372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: X / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1944TIGHT POSITIONAL0.190.05
1833MEDIUM POSITIONAL0.240.5
1944TIGHT THERMAL0.790.5
1833MEDIUM THERMAL0.922
28TIGHT POSITIONAL0.020.05
28TIGHT THERMAL0.950.5
3184MEDIUM POSITIONAL0.940.5
3184MEDIUM THERMAL4.122
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 94 -
Rwork0.246 1774 -
obs--93.03 %
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)
11.5256-1.12890.46514.4481-0.21351.5749-0.0448-0.0970.10880.0451-0.01730.303-0.06-0.1080.0620.0529-0.020.05380.2132-0.0340.112422.0914.819-29.955
26.82081.8756-3.93043.0224-2.522611.3769-0.6582-0.28240.6944-0.04020.4121-1.84360.55311.16580.24620.6797-0.0625-0.33311.3302-0.41112.425612.30968.314-29.287
32.2482-1.77981.02954.1452-1.06441.26670.0474-0.21-0.20610.30910.12080.05210.0155-0.0135-0.16820.1067-0.01950.01940.21480.01440.060145.85819.067-5.929
47.6134-1.5213-4.34419.9662-1.751311.826-0.02160.0826-0.1235-0.19710.07450.77960.2673-1.2095-0.05290.5576-0.0863-0.1530.7962-0.05560.691754.324-34.997-1.144
50.457-0.04180.16650.09060.11920.28530.0103-0.1374-0.0133-0.0662-0.00820.0147-0.0658-0.0382-0.00210.353-0.0670.14170.4132-0.00520.185535.66317.298-18.037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X68 - 309
2X-RAY DIFFRACTION1X400
3X-RAY DIFFRACTION2X315 - 343
4X-RAY DIFFRACTION3Y68 - 310
5X-RAY DIFFRACTION3Y400
6X-RAY DIFFRACTION4Y315 - 343
7X-RAY DIFFRACTION5W1 - 101

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