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- PDB-6brs: The Crystal Structure of the Ferredoxin Protease FusC in complex ... -

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Basic information

Entry
Database: PDB / ID: 6brs
TitleThe Crystal Structure of the Ferredoxin Protease FusC in complex with Arabidopsis Ferredoxin, Ethylmercury phosphate soaked dataset
Components
  • Ferredoxin-2, chloroplastic
  • Putative zinc protease
  • unidentified Ferredoxin peptide
KeywordsHYDROLASE / M16 Protease / Ferredoxin Binding / Ferredoxin Cleavage
Function / homology
Function and homology information


photosynthetic acclimation / photosynthetic electron transport chain / chloroplast / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / proteolysis / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Ferredoxin-2, chloroplastic / Zinc protease
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsGrinter, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106077/Z/14/Z United Kingdom
CitationJournal: PLoS Biol / Year: 2018
Title: FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.
Authors: Rhys Grinter / Iain D Hay / Jiangning Song / Jiawei Wang / Don Teng / Vijay Dhanesakaran / Jonathan J Wilksch / Mark R Davies / Dene Littler / Simone A Beckham / Ian R Henderson / Richard A ...Authors: Rhys Grinter / Iain D Hay / Jiangning Song / Jiawei Wang / Don Teng / Vijay Dhanesakaran / Jonathan J Wilksch / Mark R Davies / Dene Littler / Simone A Beckham / Ian R Henderson / Richard A Strugnell / Gordon Dougan / Trevor Lithgow /
Abstract: Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the ...Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the environment is often mediated by TonB-dependent transporters (TBDTs), which are β-barrel proteins that form sophisticated channels in the outer membrane. Reports of iron-bearing proteins being used as a source of iron indicate specific protein import reactions across the bacterial outer membrane. The molecular mechanism by which a folded protein can be imported in this way had remained mysterious, as did the evolutionary process that could lead to such a protein import pathway. How does the bacterium evolve the specificity factors that would be required to select and import a protein encoded on another organism's genome? We describe here a model whereby the plant iron-bearing protein ferredoxin can be imported across the outer membrane of the plant pathogen Pectobacterium by means of a Brownian ratchet mechanism, thereby liberating iron into the bacterium to enable its growth in plant tissues. This import pathway is facilitated by FusC, a member of the same protein family as the mitochondrial processing peptidase (MPP). The Brownian ratchet depends on binding sites discovered in crystal structures of FusC that engage a linear segment of the plant protein ferredoxin. Sequence relationships suggest that the bacterial gene encoding FusC has previously unappreciated homologues in plants and that the protein import mechanism employed by the bacterium is an evolutionary echo of the protein import pathway in plant mitochondria and plastids.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative zinc protease
F: Ferredoxin-2, chloroplastic
C: Ferredoxin-2, chloroplastic
E: unidentified Ferredoxin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,71012
Polymers124,4224
Non-polymers1,2888
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.531, 127.369, 132.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 2 types, 3 molecules AFC

#1: Protein Putative zinc protease


Mass: 101378.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (bacteria)
Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA0879 / Production host: Escherichia coli (E. coli) / Strain (production host): C31 (DE3) / References: UniProt: Q6D8U3
#2: Protein Ferredoxin-2, chloroplastic / AtFd2


Mass: 11342.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FD2, PETF, PETF1, At1g60950, T7P1.9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16972

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide unidentified Ferredoxin peptide


Mass: 358.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FD2, PETF, PETF1, At1g60950, T7P1.9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)

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Non-polymers , 3 types, 307 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Hg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NaKPhos, 0.1 M Bistris Propane, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 30, 2017 / Details: Yes
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→47.62 Å / Num. obs: 61936 / % possible obs: 100 % / Redundancy: 29.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.049 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 30.1 % / Rmerge(I) obs: 3.014 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4552 / CC1/2: 0.595 / Rpim(I) all: 0.788 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.645 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.242 3188 5.15 %
Rwork0.1886 --
obs0.1914 61862 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 0 20 299 7814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097756
X-RAY DIFFRACTIONf_angle_d0.92810536
X-RAY DIFFRACTIONf_dihedral_angle_d6.9046513
X-RAY DIFFRACTIONf_chiral_restr0.0521170
X-RAY DIFFRACTIONf_plane_restr0.0061380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33440.35071470.2852531X-RAY DIFFRACTION100
2.3344-2.37080.31911290.27332500X-RAY DIFFRACTION100
2.3708-2.40970.33771470.27172525X-RAY DIFFRACTION100
2.4097-2.45130.35441390.24762508X-RAY DIFFRACTION100
2.4513-2.49580.29391260.24552513X-RAY DIFFRACTION100
2.4958-2.54380.30671490.24352532X-RAY DIFFRACTION100
2.5438-2.59570.32441440.242503X-RAY DIFFRACTION100
2.5957-2.65220.29181390.24342530X-RAY DIFFRACTION100
2.6522-2.71390.31351390.2462527X-RAY DIFFRACTION100
2.7139-2.78170.32151310.24382515X-RAY DIFFRACTION100
2.7817-2.85690.25841370.21892525X-RAY DIFFRACTION100
2.8569-2.9410.26581450.212526X-RAY DIFFRACTION100
2.941-3.03590.25781370.20072557X-RAY DIFFRACTION100
3.0359-3.14430.25451080.20212565X-RAY DIFFRACTION100
3.1443-3.27020.26761330.21082542X-RAY DIFFRACTION100
3.2702-3.41890.23041720.19872511X-RAY DIFFRACTION100
3.4189-3.59910.26711410.18592553X-RAY DIFFRACTION100
3.5991-3.82440.24011430.17362554X-RAY DIFFRACTION100
3.8244-4.11950.21041390.16162572X-RAY DIFFRACTION100
4.1195-4.53360.18721380.14562585X-RAY DIFFRACTION100
4.5336-5.18860.21881220.14312608X-RAY DIFFRACTION100
5.1886-6.5330.20861350.16822638X-RAY DIFFRACTION100
6.533-41.65150.18021480.15842754X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.618 Å / Origin y: 36.3151 Å / Origin z: 17.2147 Å
111213212223313233
T0.2941 Å2-0.003 Å20.0319 Å2-0.2691 Å20.0412 Å2--0.284 Å2
L0.4621 °2-0.3554 °20.2086 °2-0.1872 °2-0.0875 °2--0.217 °2
S0.0108 Å °-0.0243 Å °-0.0904 Å °0.0374 Å °-0.0255 Å °0.0633 Å °0.0875 Å °0.0319 Å °0.0118 Å °
Refinement TLS groupSelection details: all

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