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- PDB-7kwe: Crystal structure of the catalytic domain of human PDE3A bound to... -

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Basic information

Entry
Database: PDB / ID: 7kwe
TitleCrystal structure of the catalytic domain of human PDE3A bound to DNMDP
ComponentscGMP-inhibited 3',5'-cyclic phosphodiesterase A
KeywordsHYDROLASE
Function / homology
Function and homology information


cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / estrogen binding / regulation of ribonuclease activity / positive regulation of oocyte development / regulation of meiotic nuclear division / cellular response to cGMP / oocyte maturation / positive regulation of vascular permeability / negative regulation of vascular permeability / negative regulation of cAMP-mediated signaling ...cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / estrogen binding / regulation of ribonuclease activity / positive regulation of oocyte development / regulation of meiotic nuclear division / cellular response to cGMP / oocyte maturation / positive regulation of vascular permeability / negative regulation of vascular permeability / negative regulation of cAMP-mediated signaling / 3',5'-cyclic-nucleotide phosphodiesterase / nuclear estrogen receptor activity / 3',5'-cyclic-GMP phosphodiesterase activity / cGMP-mediated signaling / cAMP-mediated signaling / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cellular response to transforming growth factor beta stimulus / apoptotic signaling pathway / lipid metabolic process / G alpha (s) signalling events / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / negative regulation of apoptotic process / membrane / metal ion binding / cytosol
Similarity search - Function
3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
ACETATE ION / : / Chem-X5M / cGMP-inhibited 3',5'-cyclic phosphodiesterase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHorner, S.W. / Garvie, C.
CitationJournal: Nat Commun / Year: 2021
Title: Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.
Authors: Colin W Garvie / Xiaoyun Wu / Malvina Papanastasiou / Sooncheol Lee / James Fuller / Gavin R Schnitzler / Steven W Horner / Andrew Baker / Terry Zhang / James P Mullahoo / Lindsay Westlake / ...Authors: Colin W Garvie / Xiaoyun Wu / Malvina Papanastasiou / Sooncheol Lee / James Fuller / Gavin R Schnitzler / Steven W Horner / Andrew Baker / Terry Zhang / James P Mullahoo / Lindsay Westlake / Stephanie H Hoyt / Marcus Toetzl / Matthew J Ranaghan / Luc de Waal / Joseph McGaunn / Bethany Kaplan / Federica Piccioni / Xiaoping Yang / Martin Lange / Adrian Tersteegen / Donald Raymond / Timothy A Lewis / Steven A Carr / Andrew D Cherniack / Christopher T Lemke / Matthew Meyerson / Heidi Greulich /
Abstract: DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated ...DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated levels of both proteins. The mechanisms by which velcrins induce complex formation, and how the PDE3A-SLFN12 complex causes cancer cell death, are not fully understood. Here, we show that PDE3A and SLFN12 form a heterotetramer stabilized by binding of DNMDP. Interactions between the C-terminal alpha helix of SLFN12 and residues near the active site of PDE3A are required for complex formation, and are further stabilized by interactions between SLFN12 and DNMDP. Moreover, we demonstrate that SLFN12 is an RNase, that PDE3A binding increases SLFN12 RNase activity, and that SLFN12 RNase activity is required for DNMDP response. This new mechanistic understanding will facilitate development of velcrin compounds into new cancer therapies.
History
DepositionNov 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
D: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
C: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
B: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,45120
Polymers172,6764
Non-polymers1,77516
Water6,467359
1
A: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
B: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
hetero molecules


  • defined by author
  • Evidence: equilibrium centrifugation, Analytical ultracentrifugation suggests a similar PDE3A construct (residues 640-1141) exist as a dimer with a Kd of 40 nM., cross-linking, Cross-linking with NHS ...Evidence: equilibrium centrifugation, Analytical ultracentrifugation suggests a similar PDE3A construct (residues 640-1141) exist as a dimer with a Kd of 40 nM., cross-linking, Cross-linking with NHS and EDC, followed by denaturing SDS-PAGE, yield bands corresponding to 2 times the mass of the monomer.
  • 87.2 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)87,22610
Polymers86,3382
Non-polymers8878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
C: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,22610
Polymers86,3382
Non-polymers8878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.210, 58.520, 157.540
Angle α, β, γ (deg.)90.000, 90.660, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLUAA669 - 10932 - 378
21LYSLYSHISHISBD669 - 10782 - 363
12ILEILEGLUGLUAA671 - 10934 - 378
22ILEILEGLUGLUCC671 - 10934 - 378
13LYSLYSGLUGLUAA669 - 10932 - 378
23LYSLYSGLUGLUDB669 - 10932 - 378
14ILEILEHISHISBD671 - 10784 - 363
24ILEILEGLUGLUCC671 - 10934 - 378
15LYSLYSHISHISBD669 - 10782 - 363
25LYSLYSGLUGLUDB669 - 10932 - 378
16ILEILEGLUGLUCC671 - 10934 - 378
26ILEILEGLUGLUDB671 - 10934 - 378

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ADCB

#1: Protein
cGMP-inhibited 3',5'-cyclic phosphodiesterase A / Cyclic GMP-inhibited phosphodiesterase A / CGI-PDE A


Mass: 43169.121 Da / Num. of mol.: 4 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Details: N-terminal glycine from cleavage with TEV protease. Residues 780 to 800 replaced with GGSGGS linker. Residues 1029 to 1067 replaced with GGSGGS linker.
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE3A / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q14432, 3',5'-cyclic-nucleotide phosphodiesterase

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Non-polymers , 5 types, 375 molecules

#2: Chemical
ChemComp-X5M / (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one


Mass: 305.352 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: MES, PEG 3350, calcium acetate / PH range: 5.7 - 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2→47.7 Å / Num. obs: 187181 / % possible obs: 94.3 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rrim(I) all: 0.057 / Net I/σ(I): 10.79
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 29075 / CC1/2: 0.64 / Rrim(I) all: 0.747 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SO2

1so2


Resolution: 2→47.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.709 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 5030 5 %RANDOM
Rwork0.1846 ---
obs0.1864 95542 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.33 Å2 / Biso mean: 49.716 Å2 / Biso min: 23.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.34 Å2
2--0.53 Å20 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 2→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11926 0 0 359 12285
Biso mean---43.19 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01312248
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711380
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.64216629
X-RAY DIFFRACTIONr_angle_other_deg1.4261.58526183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49451459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45523.242657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.089152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9511554
X-RAY DIFFRACTIONr_chiral_restr0.0930.21547
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022878
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A121040.09
12B121040.09
21A120800.09
22C120800.09
31A121050.09
32D121050.09
41B120840.1
42C120840.1
51B121470.1
52D121470.1
61C121070.09
62D121070.09
LS refinement shellResolution: 2.002→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 364 -
Rwork0.32 6913 -
all-7277 -
obs--98.05 %
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)
12.76-0.51870.28242.2370.48543.854-0.2281-0.48720.05960.15170.0475-0.14280.10170.04890.18060.08040.0643-0.04260.1004-0.01760.046-23.153-8.86241.788
21.8403-0.24821.17722.07510.63223.7121-0.14250.18730.1111-0.1214-0.02880.1771-0.22350.00870.17140.0328-0.0142-0.03270.02470.01320.0356-19.144-15.7310.621
31.59630.3321-0.24272.3953-0.34493.10640.0238-0.30890.05140.2389-0.14040.1241-0.0398-0.14080.11660.11350.01-0.02850.0804-0.03250.0317-17.891-6.326-37.022
41.5115-0.2604-0.96952.2313-0.78395.7601-0.14520.2721-0.0961-0.2273-0.1351-0.17420.35480.09190.28030.13720.0177-0.01460.1205-0.03580.0614-21.6774.05-77.575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A669 - 1093
2X-RAY DIFFRACTION2B669 - 1093
3X-RAY DIFFRACTION3C671 - 1093
4X-RAY DIFFRACTION4D669 - 1093

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