[English] 日本語
Yorodumi
- PDB-7z17: E. coli C-P lyase bound to a PhnK ABC dimer in an open conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z17
TitleE. coli C-P lyase bound to a PhnK ABC dimer in an open conformation
Components
  • (Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit ...) x 3
  • Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
  • Putative phosphonates utilization ATP-binding protein PhnK
KeywordsTRANSFERASE / protein complex / ABC / hydrolase / lyase / carbon phosphorus
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 / metal ion binding / identical protein binding
Similarity search - Function
Bacterial phosphonate metabolism protein PhnH / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-ribose-1,2-cyclic-phosphate-5-phosphate / Putative phosphonates utilization ATP-binding protein PhnK / Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG / Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH / Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI / Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsAmstrup, S.K. / Sofos, 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 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 2.0Jun 22, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / chem_comp / citation / citation_author / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.pdbx_formal_charge / _audit_author.identifier_ORCID / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Mar 8, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Revision 2.2Jul 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit 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: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,41915
Polymers280,86610
Non-polymers5545
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Negative stain
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

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

#1: Protein Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG / RPnTP synthase subunit 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) / Strain: K12 / Gene: phnG, b4101, JW4062 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
References: UniProt: P16685, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase
#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 / RPnTP synthase subunit PhnI / Ribose 1-methylphosphonate 5-triphosphate synthase nucleosidase subunit


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) / Strain: K12 / Gene: phnI, b4099, JW4060 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
References: UniProt: P16687, alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase

-
Protein , 2 types, 4 molecules DHIJ

#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) / Strain: K12 / Gene: phnJ, b4098, JW4059 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
References: UniProt: P16688, alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase
#5: Protein Putative phosphonates utilization ATP-binding protein PhnK


Mass: 31995.146 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: phnK, b4097, JW5727 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 / References: UniProt: P16678

-
Non-polymers , 2 types, 5 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-I9X / alpha-D-ribose-1,2-cyclic-phosphate-5-phosphate / [(3aR,5R,6R,6aR)-2,6-bis(oxidanyl)-2-oxidanylidene-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3,2]dioxaphosphol-5-yl]methyl dihydrogen phosphate / 5-phospho-alpha-D-ribose cyclic-1,2-phosphate


Mass: 292.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O10P2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: E. coli C-P lyase bound to a PhnK ABC dimer in an open conformation
Type: COMPLEX
Details: Post ATP hydrolysis by the ATP binding cassette (ABC) protein PhnK
Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.277 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
Details: ATP up from a concentration from 0.25 to 1.5 and MgCl2 to a concentration of 6 mM was added 15 seconds before the sample was plunge frozen
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)HEPES/KOH1
2125 mMpotassium chlorideKCl1
30.5 mMEthylenediaminetetraacetic acidEDTA1
45 mMbeta mercaptoethanolBME1
51.5 mMAdenine triphosphateATP1
66 mMMagnesium chlorideMgCl21
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was produced under ATP to ADP+Pi turnover conditions. Sample was monodisperse.
Specimen supportDetails: 10 mA in an 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: 310 K / Details: Blotting for 6-9 seconds before plunging

-
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
Details: Images were collected in movie-mode with a total of 56 frames
EM imaging opticsEnergyfilter slit width: 20 eV

-
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: 1155385 / Details: Deep picker from cryoSPARC used
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31280 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 28.7 / Space: RECIPROCAL
Atomic model buildingPDB-ID: 4XB6

4xb6


Accession code: 4XB6 / Source name: PDB / Type: experimental model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more