[English] 日本語
Yorodumi
- EMDB-37337: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37337
TitleCryo-EM structure of ClassIII Lanthipeptide modification enzyme PneKC in the presence of GTP.
Map data
Sample
  • Complex: Dimeric structure of Class III lanthipeptide modification PneKC with GTP bound to one protomer.
    • Protein or peptide: Protein kinase domain-containing protein
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
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
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 / cryo EM / Resolution: 3.77 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
DepositionAug 30, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37337.png

Downloads & links

-
Map

FileDownload / File: emd_37337.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: 0.227
Minimum - Maximum-1.1802542 - 1.9741087
Average (Standard dev.)0.0029694154 (±0.05647492)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_37337_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37337_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

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

EntireName: Dimeric structure of Class III lanthipeptide modification PneKC with GTP bound to one protomer.
Components
  • Complex: Dimeric structure of Class III lanthipeptide modification PneKC with GTP bound to one protomer.
    • Protein or peptide: Protein kinase domain-containing protein
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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

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

-
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: 100.17175 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NFNLEHPFFF TNNDYSTDTS IKYQASLPFN WHEVMNNDEW VYQYPIGKFV ERQGWKIHIS SEYNSSHELL QDVAKICHEM RIPFKHLST EDKFIMRNGK LVSRGFSGKF ITCYPNQNEL ESVLQRLESA LKQYNGPYIL SDKRWDEAPI YLRYGVFRPS R DDEKKVAI ...String:
NFNLEHPFFF TNNDYSTDTS IKYQASLPFN WHEVMNNDEW VYQYPIGKFV ERQGWKIHIS SEYNSSHELL QDVAKICHEM RIPFKHLST EDKFIMRNGK LVSRGFSGKF ITCYPNQNEL ESVLQRLESA LKQYNGPYIL SDKRWDEAPI YLRYGVFRPS R DDEKKVAI DELIVGDEVV KDERLPVFKI PKGIVPPDFL NKWLDKKDKK QGDFPFIIDN AIRFSNSGGI YNARLKEDGK KI ILKEARP YTGLGFDGTY SSEKLASECK ALKILNEWSE APKIYWHGKI WEHTFLGIEH MKGVPLNRWV TNNFPLYEVV DKT KDYLLR VSKIVEKLID LTNKFHSENV YHQDLHLGNI LVKDEDEISI IDWEQAVFSN DEKVVHKVAA PGFRAWRETL PSEI DWYGI RQIAHYLYMP LVTTSDLTYN YVSQTRIEGK KLFESLGYTR EHIDYVESLL SYLDSKCPQI ENISRKKVLK PMHEI RTIE SEQDIQDFII KLLRGFTLTY GQWRKEFQSR FFPVHYYGLN FNQGIAFSDL AILWSYQQLA KKVKNFKFDD YYEIRT QVI NEAVNNFKKS SLSGLFDGKI GTIWLIYEFG EIDRAVELFT THFIEIFENS QNKNLYSGQA GILLVGLYFL SKGEIDN KL GEEILIRLRE YTLNYIENPE TFCKVGASDV QSNDPYENFG GLLYGHAGVA WLFGEAYKLT GESIYKNGLE LAVDKELV A YKVDSNNSLQ YSQGHRLLPY LATGSAGLLL LINRNKEILS SKYLKYLTSL ERATDVVFCV LPGLFNGFCG LEVANNIYS DIDDNFSGQK KLIEQLYRYL CVIEEGFVIA GDNGLKITTD IASGFAGVAI GLVSIMDNKL TILPQI

UniProtKB: Protein kinase domain-containing protein

-
Macromolecule #2: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

Details: 25mM Tris, 200mM NaCl
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 257035
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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