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Yorodumi- EMDB-13960: Cryo-EM structure of Ldh-EtfAB complex from Acetobacterium woodii -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13960 | |||||||||
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Title | Cryo-EM structure of Ldh-EtfAB complex from Acetobacterium woodii | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information lactate dehydrogenase (NAD+,ferredoxin) / D-lactate dehydrogenase activity / FAD binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Acetobacterium woodii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.43 Å | |||||||||
Authors | Kayastha K / Ermler U | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Elife / Year: 2022 Title: Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex. Authors: Kanwal Kayastha / Alexander Katsyv / Christina Himmrich / Sonja Welsch / Jan M Schuller / Ulrich Ermler / Volker Müller / Abstract: Lactate oxidation with NAD as electron acceptor is a highly endergonic reaction. Some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) ...Lactate oxidation with NAD as electron acceptor is a highly endergonic reaction. Some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) using a lactate dehydrogenase (Ldh) in concert with the electron-transferring proteins EtfA and EtfB. The electron cryo-microscopically characterized (Ldh-EtfAB) complex of at 2.43 Å resolution consists of a mobile EtfAB shuttle domain located between the rigid central Ldh and the peripheral EtfAB base units. The FADs of Ldh and the EtfAB shuttle domain contact each other thereby forming the D (dehydrogenation-connected) state. The intermediary Glu37 and Glu139 may harmonize the redox potentials between the FADs and the pyruvate/lactate pair crucial for FBEC. By integrating Alphafold2 calculations a plausible novel B (bifurcation-connected) state was obtained allowing electron transfer between the EtfAB base and shuttle FADs. Kinetic analysis of enzyme variants suggests a correlation between NAD binding site and D-to-B-state transition implicating a 75° rotation of the EtfAB shuttle domain. The FBEC inactivity when truncating the ferredoxin domain of EtfA substantiates its role as redox relay. Lactate oxidation in Ldh is assisted by the catalytic base His423 and a metal center. On this basis, a comprehensive catalytic mechanism of the FBEC process was proposed. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13960.map.gz | 69.9 MB | EMDB map data format | |
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Header (meta data) | emd-13960-v30.xml emd-13960.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13960_fsc.xml | 13.1 KB | Display | FSC data file |
Images | emd_13960.png | 127.6 KB | ||
Masks | emd_13960_msk_1.map | 91.1 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13960 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13960 | HTTPS FTP |
-Related structure data
Related structure data | 7qh2MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13960.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13960_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ldh-EtfAB complex
Entire | Name: Ldh-EtfAB complex |
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Components |
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-Supramolecule #1: Ldh-EtfAB complex
Supramolecule | Name: Ldh-EtfAB complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Complex composed of a dimer of a trimer of EtfA, EtfB and Ldh subunits making a hexameric oligomer state. Each of the subunits contain 1 FAD co-factor making total of 6 FADs. 2 Ldh subunits ...Details: Complex composed of a dimer of a trimer of EtfA, EtfB and Ldh subunits making a hexameric oligomer state. Each of the subunits contain 1 FAD co-factor making total of 6 FADs. 2 Ldh subunits contain 1 Fe molecule each. |
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Source (natural) | Organism: Acetobacterium woodii (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: del-iscR / Recombinant plasmid: pET21a |
Molecular weight | Experimental: 220 KDa |
-Macromolecule #1: Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctC
Macromolecule | Name: Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctC type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: lactate dehydrogenase (NAD+,ferredoxin) |
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Source (natural) | Organism: Acetobacterium woodii (bacteria) / Strain: ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1 |
Molecular weight | Theoretical: 46.222496 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAGIKIIKEN VDRETFEALA EICPFDAFSY ENDKLEVTAA CKMCKMCLKK GPEGVLILEE DEKVAIDKSL YRGITVYVDH IEGQIHPVT FELIGKAREL AAVIGHPVYA LLMGTNITEK ADELLKYGVD KVFVYDKPEL KHFVIEPYAN VLEDFIEKVK P SSILVGAT ...String: MAGIKIIKEN VDRETFEALA EICPFDAFSY ENDKLEVTAA CKMCKMCLKK GPEGVLILEE DEKVAIDKSL YRGITVYVDH IEGQIHPVT FELIGKAREL AAVIGHPVYA LLMGTNITEK ADELLKYGVD KVFVYDKPEL KHFVIEPYAN VLEDFIEKVK P SSILVGAT NVGRSLAPRV AARYRTGLTA DCTILEMKEN TDLVQIRPAF GGNIMAQIVT ENTRPQFCTV RYKVFTAPER VN EPWGDVE MMDIEKAKLV SAIEVMEVIK KEKGIDLSEA ETIVAVGRGV KCEKDLDMIH EFAEKIGATV ACTRPGIEAG WFD ARLQIG LSGRTVKPKL IIALGISGAV QFAAGMQNSE YIIAINSDPK APIFNIAHCG MVGDLYEILP ELLTMIEGPE NNKD TETIS IPEAIETPER MVV |
-Macromolecule #2: Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctB
Macromolecule | Name: Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctB type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: lactate dehydrogenase (NAD+,ferredoxin) |
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Source (natural) | Organism: Acetobacterium woodii (bacteria) / Strain: ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1 |
Molecular weight | Theoretical: 29.187627 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSKILVCIKQ VPGTSNVEVD PETGVLIRDG VESKLNPYDL FGLETAFRLK EQLGGTITTL SMGPMQSKEV LMESFYMGAD EGCLLSDRK FGGADVVATS YTLAQGTKRL GDFDLIICGK QTTDGDTAQV GPEMAEFLGI PHVTNVIKIL AADEKGLTLQ M NMEESLEI ...String: MSKILVCIKQ VPGTSNVEVD PETGVLIRDG VESKLNPYDL FGLETAFRLK EQLGGTITTL SMGPMQSKEV LMESFYMGAD EGCLLSDRK FGGADVVATS YTLAQGTKRL GDFDLIICGK QTTDGDTAQV GPEMAEFLGI PHVTNVIKIL AADEKGLTLQ M NMEESLEI QRVPYPCLIT VDKDIYTPRL PSYKRKLDIS KNPEIKILTL KDMYDTNEKK YGLSGSPTQV ERIFPPESNV EK TSFEGDG KVLAKALLGI LTEKKYLG |
-Macromolecule #3: Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctD
Macromolecule | Name: Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctD type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: lactate dehydrogenase (NAD+,ferredoxin) |
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Source (natural) | Organism: Acetobacterium woodii (bacteria) / Strain: ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1 |
Molecular weight | Theoretical: 51.267797 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNYKKVEASD IAAIKELIPA ERVFVGTEIG EDFSHDELGS IHSYPEVLIK VTSTEEVSKI MKYAYEHNIP VVVRGSGTGL VGACVPLFG GIMLETTLMN NILELDTENL TVTVEPGVLL MELSKFVEEN DLFYPPDPGE KSATIAGNIS TNAGGMRAVK Y GVTRDYVR ...String: MNYKKVEASD IAAIKELIPA ERVFVGTEIG EDFSHDELGS IHSYPEVLIK VTSTEEVSKI MKYAYEHNIP VVVRGSGTGL VGACVPLFG GIMLETTLMN NILELDTENL TVTVEPGVLL MELSKFVEEN DLFYPPDPGE KSATIAGNIS TNAGGMRAVK Y GVTRDYVR GLTVVLANGE IIELGGKIVK NSSGYSLKDL VIGSEGTLCV ITKAILKLLP LPKMTLSLLI PFENISDAAG IV PKIIKSK AIPTAIEFME RQTILFAEDF LGKKFPDSSS NAYILLTFDG NTKEQVEAEY ETVANLCLAE GAKDVYIVDT VER KDSVWS ARGAFLEAIK ASTTEMDECD VVVPRNRIAE FIEFTHDLAK EMDVRIPSFG HAGDGNLHIY VCRDELCQAD WEAK LAEAM DRMYAKALTF EGLVSGEHGI GYAKRKYLLN DFGTEHLALM AGIKQTFDPK NLLNPKKVCQ MA |
-Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 6 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #5: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: pH 7.5 | |||||||||
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN / Pretreatment - Pressure: 38.0 kPa / Details: 45mA | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: Blot force of +20 and blotting time of 4 seconds before plunging. | |||||||||
Details | Sample was cross linked with 1 mM of BS3 before grid preparation. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 9788 / Average exposure time: 6.52 sec. / Average electron dose: 106.17 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7qh2: |