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- PDB-7z16: E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP a... -

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Basic information

Entry
Database: PDB / ID: 7z16
TitleE. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation
Components
  • (Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit ...) x 3
  • Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
  • Phosphonate C-P lyase system protein PhnG
  • Putative phosphonates utilization ATP-binding protein PhnK
KeywordsTRANSFERASE / protein complex / ABC / hydrolase / lyase / carbon-phosphorus / SAM
Function / homology
Function and homology information


alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / peptide transport ...alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / peptide transport / 4 iron, 4 sulfur cluster binding / lyase activity / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Phosphonate C-P lyase system, PhnL / Phosphonate C-P lyase system, PhnK / Phosphonate metabolism protein PhnI / Phosphonate metabolism PhnG / Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / Bacterial phosphonate metabolism protein (PhnI) / Phosphonate metabolism protein PhnJ / Phosphonate metabolism protein PhnG / Bacterial phosphonate metabolism, PhnH / PhnH-like superfamily ...Phosphonate C-P lyase system, PhnL / Phosphonate C-P lyase system, PhnK / Phosphonate metabolism protein PhnI / Phosphonate metabolism PhnG / Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase / Bacterial phosphonate metabolism protein (PhnI) / Phosphonate metabolism protein PhnJ / Phosphonate metabolism protein PhnG / Bacterial phosphonate metabolism, PhnH / PhnH-like superfamily / Bacterial phosphonate metabolism protein (PhnH) / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI / Phosphonate C-P lyase system protein PhnG / Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase / Putative phosphonates utilization ATP-binding protein PhnK / Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL / Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.09 Å
AuthorsAmstrup, S.K. / Sofus, N. / Karlsen, J.L. / Skjerning, R.B. / Boesen, T. / Enghild, J.J. / Hove-Jensen, B. / Brodersen, D.E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0030646 Denmark
Citation
Journal: Nat Commun / Year: 2023
Title: Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase.
Authors: Søren K Amstrup / Sui Ching Ong / Nicholas Sofos / Jesper L Karlsen / Ragnhild B Skjerning / Thomas Boesen / Jan J Enghild / Bjarne Hove-Jensen / Ditlev E Brodersen /
Abstract: In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part ...In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part of a complex, multi-step pathway, the PhnJ subunit was shown to cleave the C-P bond via a radical mechanism, however, the details of the reaction could not immediately be reconciled with the crystal structure of a 220 kDa PhnGHIJ C-P lyase core complex, leaving a significant gap in our understanding of phosphonate breakdown in bacteria. Here, we show using single-particle cryogenic electron microscopy that PhnJ mediates binding of a double dimer of the ATP-binding cassette proteins, PhnK and PhnL, to the core complex. ATP hydrolysis induces drastic structural remodelling leading to opening of the core complex and reconfiguration of a metal-binding and putative active site located at the interface between the PhnI and PhnJ subunits.
#1: Journal: Biorxiv / Year: 2022
Title: Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase
Authors: Amstrup, S.K. / Sofos, N. / Karlsen, J.L. / Skjerning, R.B. / Boesen, T. / Enghild, J.J. / Hove-Jensen, B. / Brodersen, D.E.
History
DepositionFeb 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Revision 1.2Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphonate C-P lyase system protein PhnG
B: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH
C: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI
D: Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
E: Phosphonate C-P lyase system protein PhnG
F: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH
G: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI
H: Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
I: Putative phosphonates utilization ATP-binding protein PhnK
J: Putative phosphonates utilization ATP-binding protein PhnK
K: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
L: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,85122
Polymers330,33912
Non-polymers1,51310
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Negative stain, gel filtration, Elution volume agreeing with complex size, mass spectrometry, Provide proof of each different protein in the sample
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "E"
d_2ens_1chain "A"
d_1ens_2chain "B"
d_2ens_2(chain "F" and (resid 2 through 154 or (resid 155...
d_1ens_3chain "G"
d_2ens_3chain "C"
d_1ens_4chain "D"
d_2ens_4chain "H"
d_1ens_5chain "J"
d_2ens_5chain "I"
d_1ens_6chain "L"
d_2ens_6chain "K"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAARGH1 - 144
d_21ens_1ALAARGA1 - 144
d_11ens_2THRCYSB1 - 193
d_21ens_2THRCYSI1 - 193
d_11ens_3METHISJ1 - 353
d_21ens_3METHISC1 - 353
d_11ens_4ALALYSE1 - 278
d_12ens_4ZNZNF
d_13ens_4PO4PO4G
d_21ens_4ALALYSL1 - 278
d_22ens_4ZNZNM
d_23ens_4PO4PO4N
d_11ens_5GLNASNS1 - 250
d_12ens_5MGMGT
d_13ens_5ANPANPU
d_21ens_5GLNASNO1 - 250
d_22ens_5MGMGP
d_23ens_5ANPANPQ
d_11ens_6METALAX1 - 224
d_21ens_6METALAW1 - 224

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6

NCS oper:
IDCodeMatrixVector
1given(-1), (-1), (1)401.137692728, 401.290021153
2given(-1), (-1), (1)401.143707498, 401.154260261
3given(-1), (-1), (1)401.158810175, 401.125438886
4given(-1), (-1), (1)401.119551872, 401.18867605
5given(-1), (-1), (1)401.333744656, 401.094110879
6given(-1), (-1), (1)401.693511602, 400.31697195

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Components

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Protein , 3 types, 6 molecules AEDHIJ

#1: Protein Phosphonate C-P lyase system protein PhnG


Mass: 16545.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pBW120 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phnG, I6H00_16560 / Plasmid: pET28(a) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: A0A7T2N2E5
#4: Protein Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase / PRPn C-P lyase


Mass: 31893.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pBW120 / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: phnJ, A6583_09960, A8C65_01335, A8X68_003177, ABE90_013675, ABT96_003416, ACN68_27220, ACN81_06055, ACW72_002453, AM340_04020, AMK64_003176, AO169_002527, B2D52_003427, B5N24_002958, B6L15_ ...Gene: phnJ, A6583_09960, A8C65_01335, A8X68_003177, ABE90_013675, ABT96_003416, ACN68_27220, ACN81_06055, ACW72_002453, AM340_04020, AMK64_003176, AO169_002527, B2D52_003427, B5N24_002958, B6L15_003343, BANRA_00673, BANRA_05179, BE930_16685, BE963_11965, BKD45_002102, BMT91_23195, BN17_40761, BOH76_03140, BON63_06820, BON70_15410, BvCmsHHP019_00759, BvCmsHHP056_01954, BvCmsKKP005_04467, BvCmsKKP057_05062, BZL69_05300, C6B13_11205, C6N50_000781, C7B02_13575, CBT22_003266, CCV12_000642, CCZ91_003352, CDL57_06200, CLG78_001793, CS116_003895, D3O91_17845, D9F92_14655, D9H13_21630, D9H94_23375, D9J03_04665, DAH18_16675, DAH34_17870, DEN89_17230, DEO15_07445, DIV22_19485, DTM45_21575, DU321_10015, DXT73_06970, E2127_04980, E2128_22940, E2129_04390, E5S38_10055, E5S47_14750, E5S52_04755, E5S62_09390, EC95NR1_03700, ED648_09835, EIA08_14550, EIA13_06810, EKI52_13355, ELT17_04080, ELT21_01245, ELU85_16580, ELV10_08795, ELY05_00935, ERS085366_02412, ETECE36_05287, F9407_18430, FC554_11560, G3813_002183, G5603_09230, GF699_23185, GKE84_02440, GKF52_14440, GLW94_09675, GNO40_10425, GP650_09635, GP954_07790, GQE64_23580, GQM04_25240, GQM09_07635, GSY44_18815, GUC01_08575, GW978_22970, HH411_003332, HIF90_002933, HIR12_003887, HJQ60_002653, HL425_11400, HL601_13475, HLZ20_11475, HMJ82_12545, HND12_12285, HNV65_03620, HNV94_11935, HVZ33_22655, I6H02_16305, IA00_001785, JE86ST02C_46280, JE86ST05C_46410, NCTC10974_05189, NCTC11181_01834, NCTC13148_04573, NCTC13216_02229, NCTC8960_02155, NCTC9036_04503, NCTC9706_01879, PU06_23450, RG28_25905, UN91_05940, WP4S18E08_42000
Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
References: UniProt: J7QYU2, alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase
#5: Protein Putative phosphonates utilization ATP-binding protein PhnK


Mass: 31994.162 Da / Num. of mol.: 2 / Mutation: E171Q
Source method: isolated from a genetically manipulated source
Details: pBW120 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: phnK, b4097, JW5727 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 / References: UniProt: P16678

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Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit ... , 3 types, 6 molecules BFCGKL

#2: Protein Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH / RPnTP synthase subunit PhnH


Mass: 21045.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pBW120 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: phnH, b4100, JW4061 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
References: UniProt: P16686, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase
#3: Protein Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI / Carbon-phosphorus lyase complex subunit PhnI


Mass: 38953.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pBW120 / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: phnI, BMT91_23200, DAH34_17875, DXT73_06975, E2127_04985, E2128_22935, E2129_04385, ELT21_01240, GP954_07785, HVZ33_22650, NCTC11022_04428, WP4S18E08_41990
Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
References: UniProt: A0A1V3VT92, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase
#6: Protein Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL / RPnTP synthase subunit PhnL


Mass: 24737.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pBW120 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: phnL, b4096, JW4057 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
References: UniProt: P16679, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase

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Non-polymers , 5 types, 16 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 0.327 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli) / Cellular location: Cytoplasm
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Lemo21 / Plasmid: pET28(a)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)HEPES/KOH1
2125 mMpotassium chlorideKCl1
35 mMbeta mercaptoethanolBME1
40.005 mMAdenylyl-imidodiphosphateAMPPNP1
55 mMMagnesium chlorideMgCl21
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse.
Specimen supportDetails: 10 mA GloQube, Quorum / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: Blotting for 6-9 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 135000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5666
Details: Images were collected in movie-mode with a total of 56 frames
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4cryoSPARC3.2CTF correction
9cryoSPARC3.2initial Euler assignmentAb-initio
10cryoSPARC3.2final Euler assignmentNon-uniform refinement
11cryoSPARC3.2classification3D variability
12cryoSPARC3.23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1023261 / Details: Deep picker from cryoSPARC used
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59737
Details: reconstruction using cryoSPARC homogeneous refinement
Symmetry type: POINT
Atomic model buildingB value: 28.8 / Space: RECIPROCAL
Atomic model buildingPDB-ID: 4XB6

4xb6


Accession code: 4XB6 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 34.05 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001722897
ELECTRON MICROSCOPYf_angle_d0.480831130
ELECTRON MICROSCOPYf_chiral_restr0.04573558
ELECTRON MICROSCOPYf_plane_restr0.00354093
ELECTRON MICROSCOPYf_dihedral_angle_d10.46478501
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2HELECTRON MICROSCOPYNCS constraints0.000714511096861
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.000723611365288
ens_3d_2JELECTRON MICROSCOPYNCS constraints0.000705030338718
ens_4d_2EELECTRON MICROSCOPYNCS constraints0.000703343409544
ens_5d_2IELECTRON MICROSCOPYNCS constraints0.000701389071946
ens_6d_2KELECTRON MICROSCOPYNCS constraints0.000708146149277

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