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- PDB-7z0t: Structure of the Escherichia coli formate hydrogenlyase complex (... -

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Basic information

Entry
Database: PDB / ID: 7z0t
TitleStructure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, composite structure)
Components
  • (Formate hydrogenlyase subunit ...) x 6
  • Formate dehydrogenase H
KeywordsMEMBRANE PROTEIN / FHL / group-4 membrane bound hydrogenase / [NiFe] hydrogenase
Function / homology
Function and homology information


formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / glucose catabolic process / formate dehydrogenase (NAD+) activity / anaerobic electron transport chain / urate catabolic process / molybdopterin cofactor binding / anaerobic respiration ...formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / glucose catabolic process / formate dehydrogenase (NAD+) activity / anaerobic electron transport chain / urate catabolic process / molybdopterin cofactor binding / anaerobic respiration / oxidoreductase activity, acting on NAD(P)H / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / NAD binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / : / : / : / Formate dehydrogenase H, molybdopterin-binding domain / ADC-like domains / NADH:ubiquinone oxidoreductase Nqo5 subunit / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / : ...: / : / : / : / Formate dehydrogenase H, molybdopterin-binding domain / ADC-like domains / NADH:ubiquinone oxidoreductase Nqo5 subunit / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Prokaryotic molybdopterin oxidoreductases signature 2. / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Rossmann fold - #12280 / Molybdopterin oxidoreductase Fe4S4 domain / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / N-terminal domain of TfIIb / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase / : / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / Beta Polymerase; domain 2 / Single Sheet / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / CARBONMONOXIDE-(DICYANO) IRON / : / Chem-MGD / NICKEL (II) ION / IRON/SULFUR CLUSTER / Formate dehydrogenase H / Formate hydrogenlyase subunit 2 / Formate hydrogenlyase subunit 3 / Formate hydrogenlyase subunit 4 ...: / CARBONMONOXIDE-(DICYANO) IRON / : / Chem-MGD / NICKEL (II) ION / IRON/SULFUR CLUSTER / Formate dehydrogenase H / Formate hydrogenlyase subunit 2 / Formate hydrogenlyase subunit 3 / Formate hydrogenlyase subunit 4 / Formate hydrogenlyase subunit 5 / Formate hydrogenlyase subunit 6 / Formate hydrogenlyase subunit 7
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSteinhilper, R. / Murphy, B.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli.
Authors: Ralf Steinhilper / Gabriele Höff / Johann Heider / Bonnie J Murphy /
Abstract: The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase ...The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H during fermentation, its reversibility, allowing H-dependent CO reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Formate hydrogenlyase subunit 3
E: Formate hydrogenlyase subunit 5
B: Formate hydrogenlyase subunit 2
G: Formate hydrogenlyase subunit 7
F: Formate hydrogenlyase subunit 6
D: Formate hydrogenlyase subunit 4
A: Formate dehydrogenase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,13621
Polymers313,4957
Non-polymers4,64114
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Formate hydrogenlyase subunit ... , 6 types, 6 molecules CEBGFD

#1: Protein Formate hydrogenlyase subunit 3 / FHL subunit 3 / Hydrogenase-3 component C


Mass: 64121.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P16429
#2: Protein Formate hydrogenlyase subunit 5 / FHL subunit 5 / Hydrogenase-3 component E


Mass: 66589.859 Da / Num. of mol.: 1 / Mutation: internal deca-His-Gly-Ser sequence after Gly83 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P16431
#3: Protein Formate hydrogenlyase subunit 2 / FHL subunit 2 / Hydrogenase-3 component B


Mass: 21899.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AAK1
#4: Protein Formate hydrogenlyase subunit 7 / FHL subunit 7 / Hydrogenase-3 component G


Mass: 28033.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P16433
#5: Protein Formate hydrogenlyase subunit 6 / FHL subunit 6 / Hydrogenase-3 component F


Mass: 20336.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P16432
#6: Protein Formate hydrogenlyase subunit 4 / FHL subunit 4 / Hydrogenase 3 component D


Mass: 33049.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P16430

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Protein , 1 types, 1 molecules A

#7: Protein Formate dehydrogenase H / Formate dehydrogenase-H subunit alpha / FDH-H / Formate-hydrogen-lyase-linked / selenocysteine- ...Formate dehydrogenase-H subunit alpha / FDH-H / Formate-hydrogen-lyase-linked / selenocysteine-containing polypeptide


Mass: 79465.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12
References: UniProt: P07658, formate dehydrogenase (hydrogenase)

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Non-polymers , 6 types, 14 molecules

#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia coli formate hydrogenlyase complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 72 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
7Coot0.9model fitting
10RELION3final Euler assignment
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: OTHER / Num. of particles: 90459
Details: This is a composite map. The maps that constitute this composite map have resolutions between 3.0 and 3.4 A. These have all been determined by FSC 0.143 cut-off.
Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421210
ELECTRON MICROSCOPYf_angle_d0.77328924
ELECTRON MICROSCOPYf_dihedral_angle_d6.1442917
ELECTRON MICROSCOPYf_chiral_restr0.0493297
ELECTRON MICROSCOPYf_plane_restr0.0063672

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