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- EMDB-34840: Bi-functional malonyl-CoA reductuase from Chloroflexus aurantiacus -

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Basic information

Entry
Database: EMDB / ID: EMD-34840
TitleBi-functional malonyl-CoA reductuase from Chloroflexus aurantiacus
Map data
Sample
  • Complex: Dimeric state of malonyl-CoA reductase (MCR) from Chloroflexus aurantiacus
    • Protein or peptide: Short-chain dehydrogenase/reductase SDR
Keywordsmalonyl-CoA reductase (MCR) / bi-functional enzyme / NADPH-dependent reduction / OXIDOREDUCTASE
Function / homologyfatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesChloroflexus aurantiacus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsAhn JW / Kim S
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
Other government2020R1I1A1A01057880
Other government2020M3H1A1075314 Korea, Republic Of
CitationJournal: Int J Biol Macromol / Year: 2023
Title: Cryo-EM structure of bifunctional malonyl-CoA reductase from Chloroflexus aurantiacus reveals a dynamic domain movement for high enzymatic activity.
Authors: Jae-Woo Ahn / Sangwoo Kim / Jiyeon Hong / Kyung-Jin Kim /
Abstract: The platform chemical 3-hydroxypropionic acid is used to synthesize various valuable materials, including bioplastics. Bifunctional malonyl-CoA reductase is a key enzyme in 3-hydroxypropionic acid ...The platform chemical 3-hydroxypropionic acid is used to synthesize various valuable materials, including bioplastics. Bifunctional malonyl-CoA reductase is a key enzyme in 3-hydroxypropionic acid biosynthesis as it catalyzes the two-step reduction of malonyl-CoA to malonate semialdehyde to 3-hydroxypropionic acid. Here, we report the cryo-EM structure of a full-length malonyl-CoA reductase protein from Chloroflexus aurantiacus (CaMCR). The EM model of CaMCR reveals a tandem helix architecture comprising an N-terminal (CaMCR) and a C-terminal (CaMCR) domain. The CaMCR model also revealed that the enzyme undergoes a dynamic domain movement between CaMCR and CaMCR due to the presence of a flexible linker between these two domains. Increasing the flexibility and extension of the linker resulted in a twofold increase in enzyme activity, indicating that for CaMCR, domain movement is crucial for high enzyme activity. We also describe the structural features of CaMCR and CaMCR. This study reveals the protein structures underlying the molecular mechanism of CaMCR and thereby provides valuable information for future enzyme engineering to improve the productivity of 3-hydroxypropionic acid.
History
DepositionNov 24, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34840.png

Downloads & links

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Map

FileDownload / File: emd_34840.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 4.58
Minimum - Maximum-18.97701 - 36.211426000000003
Average (Standard dev.)-0.000000000003747 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34840_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34840_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34840_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric state of malonyl-CoA reductase (MCR) from Chloroflexus au...

EntireName: Dimeric state of malonyl-CoA reductase (MCR) from Chloroflexus aurantiacus
Components
  • Complex: Dimeric state of malonyl-CoA reductase (MCR) from Chloroflexus aurantiacus
    • Protein or peptide: Short-chain dehydrogenase/reductase SDR

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Supramolecule #1: Dimeric state of malonyl-CoA reductase (MCR) from Chloroflexus au...

SupramoleculeName: Dimeric state of malonyl-CoA reductase (MCR) from Chloroflexus aurantiacus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chloroflexus aurantiacus (bacteria)
Molecular weightTheoretical: 264 KDa

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Macromolecule #1: Short-chain dehydrogenase/reductase SDR

MacromoleculeName: Short-chain dehydrogenase/reductase SDR / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus (bacteria)
Molecular weightTheoretical: 132.134219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGTGRLAGK IALITGGAGN IGSELTRRFL AEGATVIISG RNRAKLTALA ERMQAEAGVP AKRIDLEVMD GSDPVAVRAG IEAIVARHG QIDILVNNAG SAGAQRRLAE IPLTEAELGP GAEETLHASI ANLLGMGWHL MRIAAPHMPV GSAVINVSTI F SRAEYYGR ...String:
MSGTGRLAGK IALITGGAGN IGSELTRRFL AEGATVIISG RNRAKLTALA ERMQAEAGVP AKRIDLEVMD GSDPVAVRAG IEAIVARHG QIDILVNNAG SAGAQRRLAE IPLTEAELGP GAEETLHASI ANLLGMGWHL MRIAAPHMPV GSAVINVSTI F SRAEYYGR IPYVTPKAAL NALSQLAARE LGARGIRVNT IFPGPIESDR IRTVFQRMDQ LKGRPEGDTA HHFLNTMRLC RA NDQGALE RRFPSVGDVA DAAVFLASAE SAALSGETIE VTHGMELPAC SETSLLARTD LRTIDASGRT TLICAGDQIE EVM ALTGML RTCGSEVIIG FRSAAALAQF EQAVNESRRL AGADFTPPIA LPLDPRDPAT IDAVFDWAGE NTGGIHAAVI LPAT SHEPA PCVIEVDDER VLNFLADEIT GTIVIASRLA RYWQSQRLTP GARARGPRVI FLSNGADQNG NVYGRIQSAA IGQLI RVWR HEAELDYQRA SAAGDHVLPP VWANQIVRFA NRSLEGLEFA CAWTAQLLHS QRHINEITLN IPANISATTG ARSASV GWA ESLIGLHLGK VALITGGSAG IGGQIGRLLA LSGARVMLAA RDRHKLEQMQ AMIQSELAEV GYTDVEDRVH IAPGCDV SS EAQLADLVER TLSAFGTVDY LINNAGIAGV EEMVIDMPVE GWRHTLFANL ISNYSLMRKL APLMKKQGSG YILNVSSY F GGEKDAAIPY PNRADYAVSK AGQRAMAEVF ARFLGPEIQI NAIAPGPVEG DRLRGTGERP GLFARRARLI LENKRLNEL HAALIAAART DERSMHELVE LLLPNDVAAL EQNPAAPTAL RELARRFRSE GDPAASSSSA LLNRSIAAKL LARLHNGGYV LPADIFANL PNPPDPFFTR AQIDREARKV RDGIMGMLYL QRMPTEFDVA MATVYYLADR NVSGETFHPS GGLRYERTPT G GELFGLPS PERLAELVGS TVYLIGEHLT EHLNLLARAY LERYGARQVV MIVETETGAE TMRRLLHDHV EAGRLMTIVA GD QIEAAID QAITRYGRPG PVVCTPFRPL PTVPLVGRKD SDWSTVLSEA EFAELCEHQL THHFRVARKI ALSDGASLAL VTP ETTATS TTEQFALANF IKTTLHAFTA TIGVESERTA QRILINQVDL TRRARAEEPR DPHERQQELE RFIEAVLLVT APLP PEADT RYAGRIHRGR AITV

UniProtKB: Short-chain dehydrogenase/reductase SDR

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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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 20mM Tris-HCl, 150mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup model#0 - Type of model: INSILICO MODEL
#0 - In silico model: Dimeric models based on PDB code 6K8W and 6K8S predicted by the swiss-modeling group
#1 - Type of model: INSILICO MODEL
#1 - In silico model: Dimeric models based on PDB code 6K8W and 6K8S predicted by the swiss-modeling group
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85107
FSC plot (resolution estimation)

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