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- EMDB-23710: 6-Deoxyerythronolide B synthase (DEBS) hybrid module (M3/1) in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-23710
Title6-Deoxyerythronolide B synthase (DEBS) hybrid module (M3/1) in complex with antibody fragment 1B2
Map dataM3-1TE
Sample
  • Complex: Complex between DEBS M3/1TE and antibody fragment 1B2
    • Protein or peptide: 6-deoxyerythronolide-B synthase EryA2, modules 3 and 4,EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera
    • Protein or peptide: 1B2 (heavy chain)
    • Protein or peptide: 1B2 (light chain)
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Polyketide synthase, docking domain superfmaily / Zinc-binding dehydrogenase / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. ...Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Polyketide synthase, docking domain superfmaily / Zinc-binding dehydrogenase / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / GroES-like superfamily / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-deoxyerythronolide-B synthase EryA2, modules 3 and 4 / 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 / EryAI
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCogan DP / Zhang K / Chiu W / Khosla C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
CitationJournal: Science / Year: 2021
Title: Mapping the catalytic conformations of an assembly-line polyketide synthase module.
Authors: Dillon P Cogan / Kaiming Zhang / Xiuyuan Li / Shanshan Li / Grigore D Pintilie / Soung-Hun Roh / Charles S Craik / Wah Chiu / Chaitan Khosla /
Abstract: Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By ...Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.
History
DepositionMar 28, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7m7e
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23710.png

Downloads & links

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Map

FileDownload / File: emd_23710.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationM3-1TE
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.272 / Movie #1: 0.3
Minimum - Maximum-3.3485904 - 5.1633744
Average (Standard dev.)0.0010220226 (±0.06085146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ376376376
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-3.3495.1630.001

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Supplemental data

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Sample components

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Entire : Complex between DEBS M3/1TE and antibody fragment 1B2

EntireName: Complex between DEBS M3/1TE and antibody fragment 1B2
Components
  • Complex: Complex between DEBS M3/1TE and antibody fragment 1B2
    • Protein or peptide: 6-deoxyerythronolide-B synthase EryA2, modules 3 and 4,EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera
    • Protein or peptide: 1B2 (heavy chain)
    • Protein or peptide: 1B2 (light chain)

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Supramolecule #1: Complex between DEBS M3/1TE and antibody fragment 1B2

SupramoleculeName: Complex between DEBS M3/1TE and antibody fragment 1B2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 430 KDa

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Macromolecule #1: 6-deoxyerythronolide-B synthase EryA2, modules 3 and 4,EryAI,6-de...

MacromoleculeName: 6-deoxyerythronolide-B synthase EryA2, modules 3 and 4,EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 6-deoxyerythronolide-B synthase
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 187.835422 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASTDSEKVA EYLRRATLDL RAARQRIREL ESDPIAIVSM ACRLPGGVNT PQRLWELLRE GGETLSGFPT DRGWDLARLH HPDPDNPGT SYVDKGGFLD DAAGFDAEFF GVSPREAAAM DPQQRLLLET SWELVENAGI DPHSLRGTAT GVFLGVAKFG Y GEDTAAAE ...String:
MASTDSEKVA EYLRRATLDL RAARQRIREL ESDPIAIVSM ACRLPGGVNT PQRLWELLRE GGETLSGFPT DRGWDLARLH HPDPDNPGT SYVDKGGFLD DAAGFDAEFF GVSPREAAAM DPQQRLLLET SWELVENAGI DPHSLRGTAT GVFLGVAKFG Y GEDTAAAE DVEGYSVTGV APAVASGRIS YTMGLEGPSI SVDTACSSSL VALHLAVESL RKGESSMAVV GGAAVMATPG VF VDFSRQR ALAADGRSKA FGAGADGFGF SEGVTLVLLE RLSEARRNGH EVLAVVRGSA LNQDGASNGL SAPSGPAQRR VIR QALESC GLEPGDVDAV EAHGTGTALG DPIEANALLD TYGRDRDADR PLWLGSVKSN IGHTQAAAGV TGLLKVVLAL RNGE LPATL HVEEPTPHVD WSSGGVALLA GNQPWRRGER TRRARVSAFG ISGTNAHVIV EEAPEREHRE TTAHDGRPVP LVVSA RTTA ALRAQAAQIA ELLERPDADL AGVGLGLATT RARHEHRAAV VASTREEAVR GLREIAAGAA TADAVVEGVT EVDGRN VVF LFPGQGSQWA GMGAELLSSS PVFAGKIRAC DESMAPMQDW KVSDVLRQAP GAPGLDRVDV VQPVLFAVMV SLAELWR SY GVEPAAVVGH SQGEIAAAHV AGALTLEDAA KLVVGRSRLM RSLSGEGGMA AVALGEAAVR ERLRPWQDRL SVAAVNGP R SVVVSGEPGA LRAFSEDCAA EGIRVRDIDV DYASHSPQIE RVREELLETT GDIAPRPARV TFHSTVESRS MDGTELDAR YWYRNLRETV RFADAVTRLA ESGYDAFIEV SPHPVVVQAV EEAVEEADGA EDAVVVGSLH RDGGDLSAFL RSMATAHVSG VDIRWDVAL PGAAPFALPT YPFQRKRYWL QPAAPAAASD ELAYRIEWRP TGAGEPARLD GTWLVAKYAG TADETSTAAR E ALESAGAR VRELVVDARC GRDELAERLR SVGEVAGVLS LLAVDEAEPE EAPLALASLA DTLSLVQAMV SAELGCPLWT VT ESAVATG PFERVRNAAH GALWGVGRVI ALENPAVWGG LVDVPAGSVA ELARHLAAVV SGGAGEDQLA LRADGVYGRR WVR AAAPAT DDEWKPTGTV LVTGGTGGVG GQIARWLARR GAPHLLLVSR SGPDADGAGE LVAELEALGA RTTVAACDVT DRES VRELL GGIGDDVPLS AVFHAAATLD DGTVDTLTGE RIERASRAKV LGARNLHELT RELDLTAFVL FSSFASAFGA PGLGG YAPG NAYLDGLAQQ RRSDGLPATA VAWGTWAGSG MAEGPVADRF RRHGVIEMPP ETACRALQNA LDRAEVCPIV IDVRWD RFL LAYTAQRPTR LFDEIDDARR AAPQAAAEPR VGALASLPAP EREKALFELV RSHAAAVLGH ASAERVPADQ AFAELGV DS LSALELRNRL GAATGVRLPT TTVFDHPDVR TLAAHLAAEL GSGTPAREAS SALRDGYRQA GVSGRVRSYL DLLAGLSD F REHFDGSDGF SLDLVDMADG PGEVTVICCA GTAAISGPHE FTRLAGALRG IAPVRAVPQP GYEEGEPLPS SMAAVAAVQ ADAVIRTQGD KPFVVAGHSA GALMAYALAT ELLDRGHPPR GVVLIDVYPP GHQDAMNAWL EELTATLFDR ETVRMDDTRL TALGAYDRL TGQWRPRETG LPTLLVSAGE PMGPWPDDSW KPTWPFEHDT VAVPGDHFTM VQEHADAIAR HIDAWLGGGN S SSVDKLAA ALEHHHHHH

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Macromolecule #2: 1B2 (heavy chain)

MacromoleculeName: 1B2 (heavy chain) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.447611 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEVQLVQSG GGLVQPGRSL RLSCTASGFT FGDYAMSWVR QAPGKGLEWV GFIRSKAYGG TTEYAASVKG RFTISRDDSK SIAYLQMNS LKTEDTAVYY CTRGGTLFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
MAEVQLVQSG GGLVQPGRSL RLSCTASGFT FGDYAMSWVR QAPGKGLEWV GFIRSKAYGG TTEYAASVKG RFTISRDDSK SIAYLQMNS LKTEDTAVYY CTRGGTLFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCAALVP RGSAHHHHHH AA DYKDDDD KA

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Macromolecule #3: 1B2 (light chain)

MacromoleculeName: 1B2 (light chain) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.715832 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQSLLHSNG YNYLDWYLQK PGQSPQLLIY LGSNRASGVP DRFSGSGSG TDFTLKISRV EAEDVGVYYC MQSLQTPRLT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPRGAKV ...String:
LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQSLLHSNG YNYLDWYLQK PGQSPQLLIY LGSNRASGVP DRFSGSGSG TDFTLKISRV EAEDVGVYYC MQSLQTPRLT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPRGAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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

Concentration10 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
100.0 mMC6H8O7citric acid
100.0 mMNaClSodium chloridesodium chloride
10.0 mMC8H18N2O4SHEPES
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3974 / Average exposure time: 8.5 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 381647
CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93053

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