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- PDB-4m6r: Structural and biochemical basis for the inhibition of cell death... -

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Basic information

Entry
Database: PDB / ID: 4m6r
TitleStructural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme
ComponentsMethylthioribulose-1-phosphate dehydratase
KeywordsLYASE / APIP / MtnB / Class II aldolase family / dehydratase
Function / homology
Function and homology information


methylthioribulose 1-phosphate dehydratase / methylthioribulose 1-phosphate dehydratase activity / Methionine salvage pathway / Formation of apoptosome / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / Regulation of the apoptosome activity / pyroptosis / regulation of ERK1 and ERK2 cascade / protein homotetramerization ...methylthioribulose 1-phosphate dehydratase / methylthioribulose 1-phosphate dehydratase activity / Methionine salvage pathway / Formation of apoptosome / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / Regulation of the apoptosome activity / pyroptosis / regulation of ERK1 and ERK2 cascade / protein homotetramerization / apoptotic process / negative regulation of apoptotic process / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Methylthioribulose-1-phosphate dehydratase, eukaryotes / Methylthioribulose-1-phosphate dehydratase / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methylthioribulose-1-phosphate dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKang, W. / Hong, S.H. / Lee, H.M. / Kim, N.Y. / Lim, Y.C. / Le, L.T.M. / Lim, B. / Kim, H.C. / Kim, T.Y. / Ashida, H. ...Kang, W. / Hong, S.H. / Lee, H.M. / Kim, N.Y. / Lim, Y.C. / Le, L.T.M. / Lim, B. / Kim, H.C. / Kim, T.Y. / Ashida, H. / Yokota, A. / Hah, S.S. / Chun, K.H. / Jung, Y.K. / Yang, J.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme.
Authors: Kang, W. / Hong, S.H. / Lee, H.M. / Kim, N.Y. / Lim, Y.C. / Le, L.T.M. / Lim, B. / Kim, H.C. / Kim, T.Y. / Ashida, H. / Yokota, A. / Hah, S.S. / Chun, K.H. / Jung, Y.K. / Yang, J.K.
History
DepositionAug 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_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_ref_seq_dif.details / _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
A: Methylthioribulose-1-phosphate dehydratase
B: Methylthioribulose-1-phosphate dehydratase
C: Methylthioribulose-1-phosphate dehydratase
D: Methylthioribulose-1-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4838
Polymers101,2214
Non-polymers2624
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-191 kcal/mol
Surface area33500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.035, 107.735, 192.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C

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
11LYSLYSASNASN2AA21 - 1823 - 164
21LYSLYSASNASN2BB21 - 1823 - 164
31LYSLYSASNASN2CC21 - 1823 - 164
41LYSLYSASNASN2DD21 - 1823 - 164
12TYRTYRSERSER2AA184 - 232166 - 214
22TYRTYRSERSER2BB184 - 232166 - 214
32TYRTYRSERSER2CC184 - 232166 - 214
42TYRTYRSERSER2DD184 - 232166 - 214
13GLNGLNVALVAL4AA233 - 242215 - 224
23GLNGLNVALVAL4BB233 - 242215 - 224
33GLNGLNVALVAL4CC233 - 242215 - 224

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Methylthioribulose-1-phosphate dehydratase / MTRu-1-P dehydratase / APAF1-interacting protein / hAPIP


Mass: 25305.297 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 20-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APIP, CGI-29 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96GX9, methylthioribulose 1-phosphate dehydratase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04M citric acid, 0.06M bis-tris propane, 5%(v/v) glycerol, 21%(w/v) PEG 3350, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00000, 0.91977, 0.91957, 0.90633
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.919771
30.919571
40.906331
ReflectionResolution: 2→96.05 Å / Num. obs: 72069 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 81.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.302 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22027 3616 5 %RANDOM
Rwork0.18098 ---
all0.18294 ---
obs0.18294 68405 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---1.4 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7049 0 4 567 7620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0227221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9679742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74424.211304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.153151313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7881532
X-RAY DIFFRACTIONr_chiral_restr0.210.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215396
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_it1.2161.54438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16827177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.07232783
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9694.52565
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A648tight positional0.070.05
11B648tight positional0.080.05
11C648tight positional0.080.05
11D648tight positional0.070.05
22A196tight positional0.070.05
22B196tight positional0.050.05
22C196tight positional0.060.05
22D196tight positional0.060.05
11A628medium positional0.070.5
11B628medium positional0.090.5
11C628medium positional0.080.5
11D628medium positional0.080.5
22A199medium positional0.080.5
22B199medium positional0.070.5
22C199medium positional0.070.5
22D199medium positional0.070.5
33A71medium positional0.240.5
33B71medium positional0.150.5
33C71medium positional0.240.5
11A648tight thermal0.320.5
11B648tight thermal0.50.5
11C648tight thermal0.430.5
11D648tight thermal0.390.5
22A196tight thermal0.420.5
22B196tight thermal0.470.5
22C196tight thermal0.510.5
22D196tight thermal0.580.5
11A628medium thermal0.342
11B628medium thermal0.412
11C628medium thermal0.432
11D628medium thermal0.362
22A199medium thermal0.382
22B199medium thermal0.442
22C199medium thermal0.52
22D199medium thermal0.482
33A71medium thermal3.292
33B71medium thermal2.892
33C71medium thermal6.062
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 219 -
Rwork0.219 4122 -
obs--79.37 %

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