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- PDB-4fmn: Structure of the C-terminal domain of the Saccharomyces cerevisia... -

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Basic information

Entry
Database: PDB / ID: 4fmn
TitleStructure of the C-terminal domain of the Saccharomyces cerevisiae MUTL alpha (MLH1/PMS1) heterodimer bound to a fragment of NTG2
Components
  • (DNA mismatch repair protein ...) x 2
  • DNA repair peptide
KeywordsHYDROLASE / Mismatch repair / MUTL / endonuclease / Zn-binding protein / DNA damage / DNA repair
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / MutLalpha complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / base-excision repair, AP site formation / mismatched DNA binding ...Cleavage of the damaged pyrimidine / meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / MutLalpha complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / base-excision repair, AP site formation / mismatched DNA binding / reciprocal meiotic recombination / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / ATP-dependent DNA damage sensor activity / mismatch repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Endonuclease III-like protein 1 / DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / Endonuclease III-like, conserved site-2 / Endonuclease III family signature. / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain ...Endonuclease III-like protein 1 / DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / Endonuclease III-like, conserved site-2 / Endonuclease III family signature. / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / Endonuclease III-like, iron-sulphur cluster loop motif / FES / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA mismatch repair protein PMS1 / DNA mismatch repair protein MLH1 / Endonuclease III homolog 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsGueneau, E. / Legrand, P. / Charbonnier, J.B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of the MutL alpha C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site.
Authors: Gueneau, E. / Dherin, C. / Legrand, P. / Tellier-Lebegue, C. / Gilquin, B. / Bonnesoeur, P. / Londino, F. / Quemener, C. / Le Du, M.H. / Marquez, J.A. / Moutiez, M. / Gondry, M. / Boiteux, S. / Charbonnier, J.B.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Structure summary
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / 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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein MLH1
B: DNA mismatch repair protein PMS1
C: DNA repair peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,23616
Polymers62,2733
Non-polymers96413
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-28 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.940, 66.300, 74.110
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA mismatch repair protein ... , 2 types, 2 molecules AB

#1: Protein DNA mismatch repair protein MLH1 / MutL protein homolog 1 / Post meiotic segregation protein 2


Mass: 33239.102 Da / Num. of mol.: 1 / Fragment: UNP residues 483-769
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MLH1, PMS2, YMR167W, YM8520.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P38920
#2: Protein DNA mismatch repair protein PMS1 / Postmeiotic segregation protein 1


Mass: 27948.195 Da / Num. of mol.: 1 / Fragment: UNP residues 635-873
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PMS1, YNL082W, N2317 / Production host: Escherichia coli (E. coli) / References: UniProt: P14242

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide DNA repair peptide / Ntg2 (DNA N-glycosylase and apurinic or apyrimidinic lyase)


Mass: 1085.342 Da / Num. of mol.: 1 / Fragment: UNP residues 22-29 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08214

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Non-polymers , 4 types, 144 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 25931 / Num. obs: 25750 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 66.07 Å2 / Rsym value: 0.098
Reflection shellResolution: 2.69→2.86 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.768 / % possible all: 96.8

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E4W

4e4w


Resolution: 2.69→31.63 Å / Cor.coef. Fo:Fc: 0.9421 / Cor.coef. Fo:Fc free: 0.9315 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 1305 5.07 %RANDOM
Rwork0.1686 ---
obs0.1698 25738 99.02 %-
Displacement parametersBiso mean: 85.23 Å2
Baniso -1Baniso -2Baniso -3
1--23.6993 Å20 Å26.1161 Å2
2--13.8889 Å20 Å2
3---9.8104 Å2
Refine analyzeLuzzati coordinate error obs: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2.69→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 56 131 4124
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185456HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1473SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes565HARMONIC5
X-RAY DIFFRACTIONt_it4061HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion19.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion517SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4490SEMIHARMONIC4
LS refinement shellResolution: 2.69→2.8 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2487 124 4.6 %
Rwork0.2136 2569 -
all0.2152 2693 -
obs--99.02 %
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)
10.6430.24020.99381.63050.72523.6307-0.0168-0.08940.0404-0.0481-0.0193-0.07480.0128-0.22530.0360.06240.00530.0588-0.47830.0117-0.407547.1686-0.618116.0476
21.8927-0.47322.07151.6547-0.6485.9562-0.00370.05270.116-0.1205-0.0780.61510.179-1.14890.0817-0.10020.001-0.046-0.2757-0.0196-0.239724.6723.0139-22.7475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|505 - A|769 }A505 - 769
2X-RAY DIFFRACTION2{ B|651 - B|873 }B651 - 873

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