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- EMDB-14795: Ketosynthase domain of module 3 from Brevibacillus Brevis orphan BGC11 -

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Basic information

Entry
Database: EMDB / ID: EMD-14795
TitleKetosynthase domain of module 3 from Brevibacillus Brevis orphan BGC11
Map data
Sample
  • Complex: Ketosynthase domain 3 of Brevibacillus Brevis BGC 11
    • Protein or peptide: Putative polyketide synthase
KeywordsKetosynthase / polyketide synthase / thiolase fold / Claisen Condensation / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding
Similarity search - Function
RhiE-like, KS-MAT linker domain / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...RhiE-like, KS-MAT linker domain / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / : / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis NBRC 100599 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsTittes YU / Herbst DA / Jakob RP / Maier T
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation179323, 159696, 177084 Switzerland
CitationJournal: Sci Adv / Year: 2022
Title: The structure of a polyketide synthase bimodule core.
Authors: Yves U Tittes / Dominik A Herbst / Solène F X Martin / Hugo Munoz-Hernandez / Roman P Jakob / Timm Maier /
Abstract: Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile ...Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile families of PKSs are organized as assembly lines of functional modules. Each module performs one round of precursor extension and optional modification, followed by directed transfer of the intermediate to the next module. While enzymatic domains and even modules of PKSs are well understood, the higher-order modular architecture of PKS assembly lines remains elusive. Here, we visualize a PKS bimodule core using cryo-electron microscopy and resolve a two-dimensional meshwork of the bimodule core formed by homotypic interactions between modules. The sheet-like organization provides the framework for efficient substrate transfer and for sequestration of trans-acting enzymes required for polyketide production.
History
DepositionApr 19, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14795.png

Downloads & links

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Map

FileDownload / File: emd_14795.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.9232581 - 2.9082015
Average (Standard dev.)0.00034402474 (±0.052787017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 338.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14795_msk_1.map
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Half map: #2

Fileemd_14795_half_map_1.map
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Half map: #1

Fileemd_14795_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ketosynthase domain 3 of Brevibacillus Brevis BGC 11

EntireName: Ketosynthase domain 3 of Brevibacillus Brevis BGC 11
Components
  • Complex: Ketosynthase domain 3 of Brevibacillus Brevis BGC 11
    • Protein or peptide: Putative polyketide synthase

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Supramolecule #1: Ketosynthase domain 3 of Brevibacillus Brevis BGC 11

SupramoleculeName: Ketosynthase domain 3 of Brevibacillus Brevis BGC 11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brevibacillus brevis NBRC 100599 (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Putative polyketide synthase

MacromoleculeName: Putative polyketide synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Brevibacillus brevis NBRC 100599 (bacteria) / Strain: 47 / JCM 6285 / NBRC 100599
Molecular weightTheoretical: 187.424781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSPSSVVRDV AIIGLSGRYP QAKNVDEFWN RLKEGKNCIS EIPKDRWDWQ SFFDEEKGKK ESMYTKWGGF IDDMDKFDPL FFQISPKEA EEMDPQERLF LQEAYASIED AGYTPTTLCE SRKVGVFVGV MNGNYPTGAT YWSIANRLSY LLNFQGPSVA V DTACSASL ...String:
GSPSSVVRDV AIIGLSGRYP QAKNVDEFWN RLKEGKNCIS EIPKDRWDWQ SFFDEEKGKK ESMYTKWGGF IDDMDKFDPL FFQISPKEA EEMDPQERLF LQEAYASIED AGYTPTTLCE SRKVGVFVGV MNGNYPTGAT YWSIANRLSY LLNFQGPSVA V DTACSASL TAIHFALESL YSGTSECAIA GGVNLIVDPV HYMKLSALTM LSPSNQCKSF GDQADGFVDG EGVGAIVLKP LD KAIADGD HIYGVIKGSM MNAGGKTNGY TVPNPQAQAQ LVADALQRAN VHARTVSYLE AHGTGTELGD PIEVAGLTRA FEK DTQDKQ FCALGSAKSN IGHCESAAGI AGVTKILLQL KHAQLVPSLH SRTLNPNIDF TKTPFVVQQE LAEWRRPIVE INGT TNEYP RIAGISSFGA GGSNAHVIIE EYIPEEQKQS SLKITPQNPA IFVLSAKNAE RLYEIVQQLL AFIQEHSLSD EHLAD MAYT LQVGRVAMEE RIAVIAGTMK ELQQKLTAYV KGQEHIADLY RGQVNRNQEM LDILTSDDEL EETIARWMER GKYSKL LDL WVKGLSIDWN KLYQEEQPGR ISLPTYPFAK ESYWTHARSV SSSTGVGVIH PFLHQNTSDF MEQRFSSMFT GQEFFLS DH VIKGQRVLPS AAYLEMARAA IQQATGGLDS ERELEGLRFK NVVWTQPLAV GPEPVQAHIE LYPEANGEIV FEIYSDSK Q DRDQTTEIVH SQGSAVLCSI PDIPSFDLSV LQEQCSLRTL SAEQCYDAFK KMGVDYGPAH RGIEQILIGQ EQVLAKLSL PSSVVKTQGQ FGLHPSLLDA ALQSSLGLMM ATSDFSLILP FALEEMVIVG DCSSSMWALI RYREGSKAGD RVEKFDIDLC DENGNVQVR MKGFSTRKIA NVSVRSEVEV PKASVPLEEE KAIDSSSLME QATPYFKKLL SSVIKLPANK MEADASLEKY G VDSIVAMQ MTKELEKQFG SLPKTLFFEY QTIKELTGYF LENYRENLMH ILGMRENAEA SLTQESEATM VDEVKAQTER RS KKRKSQR FASLRMETQP PKGALDIAII GISGRYPQAR NIHDFWKNLR DGKDCITEIP KDRWDHSLYF DEAKDKLGKS YSK WGGFID GVDQFDPLFF HISPREAELM DPQERLFLQC VYETIEDAGY TRETLGKHEG LGGNVGVYVG VMYEEYQLYA SAEQ ALGRA LAIAGSPASI ANRVSYFCNF HGPSMAVDTM CSSSLTGIHL ACHSLQRGEC EVAIAGGVNV SIHPNKYLYL SQGKF ASSK GRCESFGEGG DGYVPGEGVG AVLLKPLARA IADGDHIYGV IKGSAINHGG KTNGYTVPNP HSQSRVIRRA FEEAGI HPR TVSYIEAHGT GTSLGDPIEI AGLTKTFQEY TKENQFCAIG SAKSNIGHGE SAAGIAGLTK ILLQMKYKRL VPSLHSR TL NPNIDFSKTP FVVQQELAEW KRPVIEIDGV TREYARIAGI SSFGAGGANA HLVIEEYIEA EHRPPSSISS KNPAVIVL S AKNKDRLREQ VQRLLSAIRE QVLTDNDLAE IAYTLQVGRE AMEERFAVIV KSISELEAKL TYYLKDEADS PDLFTGQVK RNKETMDVFA ADEDLQQAID TWITKGKYAK ILQMWVQGLI FDWNKLYGDT KPRRISLPAY PFARERYWLP KVESQAIGLT AGEPAYLHP L

UniProtKB: Putative polyketide synthase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.18 mg/mL
BufferpH: 7.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio reconstruction in cryosparc.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182315
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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