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- EMDB-37514: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme P... -

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Basic information

Entry
Database: EMDB / ID: EMD-37514
TitleCryo-EM structure of ClassIII Lanthipeptide modification enzyme PneKC in the presence of PneA and GTPrS.
Map data
Sample
  • Complex: Dimeric structure of Class III lanthipeptide modification PneKC with GSP and PneA bound to one protomer.
    • Protein or peptide: Protein kinase domain-containing protein
  • Protein or peptide: SapB/AmfS family lantipeptide
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: water
KeywordsLanthibiotic / RiPPs / LanKC / CryoEM / Antimicrobial peptides / Antiviral peptides. / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


peptide modification / protein kinase activity / ATP binding
Similarity search - Function
RamC, N-terminal domain / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / : / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein kinase domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / Resolution: 3.7 Å
AuthorsLi Y / Luo M / Shao K / Li J
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Nat Commun / Year: 2024
Title: Mechanistic insights into lanthipeptide modification by a distinct subclass of LanKC enzyme that forms dimers.
Authors: Yifan Li / Kai Shao / Zhaoxing Li / Kongfu Zhu / Bee Koon Gan / Jian Shi / Yibei Xiao / Min Luo /
Abstract: Naturally occurring lanthipeptides, peptides post-translationally modified by various enzymes, hold significant promise as antibiotics. Despite extensive biochemical and structural studies, the ...Naturally occurring lanthipeptides, peptides post-translationally modified by various enzymes, hold significant promise as antibiotics. Despite extensive biochemical and structural studies, the events preceding peptide modification remain poorly understood. Here, we identify a distinct subclass of lanthionine synthetase KC (LanKC) enzymes with distinct structural and functional characteristics. We show that PneKC, a member of this subclass, forms a dimer and possesses GTPase activity. Through three cryo-EM structures of PneKC, we illustrate different stages of peptide PneA binding, from initial recognition to full binding. Our structures show the kinase domain complexed with the PneA core peptide and GTPγS, a phosphate-bound lyase domain, and an unconventional cyclase domain. The leader peptide of PneA interact with a gate loop, transitioning from an extended to a helical conformation. We identify a dimerization hot spot and propose a "negative cooperativity" mechanism toggling the enzyme between tense and relaxed conformation. Additionally, we identify an important salt bridge in the cyclase domain, differing from those in in conventional cyclase domains. These residues are highly conserved in the LanKC subclass and are part of two signature motifs. These results unveil potential differences in lanthipeptide modification enzymes assembly and deepen our understanding of allostery in these multifunctional enzymes.
History
DepositionSep 22, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37514.png

Downloads & links

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Map

FileDownload / File: emd_37514.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.322
Minimum - Maximum-1.4270172 - 2.0731173
Average (Standard dev.)0.0035147152 (±0.07825708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37514_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37514_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric structure of Class III lanthipeptide modification PneKC w...

EntireName: Dimeric structure of Class III lanthipeptide modification PneKC with GSP and PneA bound to one protomer.
Components
  • Complex: Dimeric structure of Class III lanthipeptide modification PneKC with GSP and PneA bound to one protomer.
    • Protein or peptide: Protein kinase domain-containing protein
  • Protein or peptide: SapB/AmfS family lantipeptide
  • Ligand: MAGNESIUM ION
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: water

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Supramolecule #1: Dimeric structure of Class III lanthipeptide modification PneKC w...

SupramoleculeName: Dimeric structure of Class III lanthipeptide modification PneKC with GSP and PneA bound to one protomer.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Protein kinase domain-containing protein

MacromoleculeName: Protein kinase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 100.581195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDYNFNLEHP FFFTNNDYST DTSIKYQASL PFNWHEVMNN DEWVYQYPIG KFVERQGWKI HISSEYNSSH ELLQDVAKIC HEMRIPFKH LSTEDKFIMR NGKLVSRGFS GKFITCYPNQ NELESVLQRL ESALKQYNGP YILSDKRWDE APIYLRYGVF R PSRDDEKK ...String:
MDYNFNLEHP FFFTNNDYST DTSIKYQASL PFNWHEVMNN DEWVYQYPIG KFVERQGWKI HISSEYNSSH ELLQDVAKIC HEMRIPFKH LSTEDKFIMR NGKLVSRGFS GKFITCYPNQ NELESVLQRL ESALKQYNGP YILSDKRWDE APIYLRYGVF R PSRDDEKK VAIDELIVGD EVVKDERLPV FKIPKGIVPP DFLNKWLDKK DKKQGDFPFI IDNAIRFSNS GGIYNARLKE DG KKIILKE ARPYTGLGFD GTYSSEKLAS ECKALKILNE WSEAPKIYWH GKIWEHTFLG IEHMKGVPLN RWVTNNFPLY EVV DKTKDY LLRVSKIVEK LIDLTNKFHS ENVYHQDLHL GNILVKDEDE ISIIDWEQAV FSNDEKVVHK VAAPGFRAWR ETLP SEIDW YGIRQIAHYL YMPLVTTSDL TYNYVSQTRI EGKKLFESLG YTREHIDYVE SLLSYLDSKC PQIENISRKK VLKPM HEIR TIESEQDIQD FIIKLLRGFT LTYGQWRKEF QSRFFPVHYY GLNFNQGIAF SDLAILWSYQ QLAKKVKNFK FDDYYE IRT QVINEAVNNF KKSSLSGLFD GKIGTIWLIY EFGEIDRAVE LFTTHFIEIF ENSQNKNLYS GQAGILLVGL YFLSKGE ID NKLGEEILIR LREYTLNYIE NPETFCKVGA SDVQSNDPYE NFGGLLYGHA GVAWLFGEAY KLTGESIYKN GLELAVDK E LVAYKVDSNN SLQYSQGHRL LPYLATGSAG LLLLINRNKE ILSSKYLKYL TSLERATDVV FCVLPGLFNG FCGLEVANN IYSDIDDNFS GQKKLIEQLY RYLCVIEEGF VIAGDNGLKI TTDIASGFAG VAIGLVSIMD NKLTILPQI

UniProtKB: Protein kinase domain-containing protein

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Macromolecule #2: SapB/AmfS family lantipeptide

MacromoleculeName: SapB/AmfS family lantipeptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 4.880407 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FQGMAEEVLN LQLVSVQVDE TDEVDGMRFS TFSTNRCGN(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

MacromoleculeName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GSP
Molecular weightTheoretical: 539.246 Da
Chemical component information

ChemComp-GSP:
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
25.0 mM(HOCH2)3CNH2Tris

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133078
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133078
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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