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- EMDB-18688: Cryo-EM structure of Apo coproheme decarboxylase from Corynebacte... -

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Basic information

Entry
Database: EMDB / ID: EMD-18688
TitleCryo-EM structure of Apo coproheme decarboxylase from Corynebacterium diphtheria.
Map data
Sample
  • Complex: Structure of Apo coproheme decarboxylase from Corynebacterium diphtheria
    • Protein or peptide: Coproheme decarboxylase
  • Ligand: water
KeywordsHeme Binding protein / Heme Biosynthesis / Actinobacteria / OXIDOREDUCTASE
Function / homologyoxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / hydrogen peroxide-dependent heme synthase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / heme B biosynthetic process / Dimeric alpha-beta barrel / heme binding / metal ion binding / Coproheme decarboxylase
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsPatil G / Guo Y / Borek D / Hofbauer S
Funding support Austria, 3 items
OrganizationGrant numberCountry
Austrian Science FundP34934 Austria
Austrian Science FundP36967 Austria
Austrian Science FundW1224 Austria
CitationJournal: Protein Sci / Year: 2025
Title: Insights into the flexibility of the domain-linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations.
Authors: Gaurav Patil / Diego Javier Alonso de Armiño / Yirui Guo / Paul G Furtmüller / Dominika Borek / Dario A Estrin / Stefan Hofbauer /
Abstract: Prokaryotic heme biosynthesis in Gram-positive bacteria follows the coproporphyrin-dependent heme biosynthesis pathway. The last step in this pathway is catalyzed by the enzyme coproheme ...Prokaryotic heme biosynthesis in Gram-positive bacteria follows the coproporphyrin-dependent heme biosynthesis pathway. The last step in this pathway is catalyzed by the enzyme coproheme decarboxylase, which oxidatively transforms two propionate groups into vinyl groups yielding heme b. The catalytic reaction cycle of coproheme decarboxylases exhibits four different states: the apo-form, the substrate (coproheme)-bound form, a transient three-propionate intermediate form (monovinyl, monopropionate deuteroheme; MMD), and the product (heme b)-bound form. In this study, we used cryogenic electron microscopy single-particle reconstruction (cryo-EM SPR) to characterize structurally the apo and heme b-bound forms of actinobacterial coproheme decarboxylase from Corynebacterium diphtheriae. The flexible loop that connects the N-terminal and the C-terminal ferredoxin domains of coproheme decarboxylases plays an important role in interactions between the enzyme and porphyrin molecule. To understand the role of this flexible loop, we performed molecular dynamics simulations on the apo and heme b coproheme decarboxylase from Corynebacterium diphtheriae. Our results are discussed in the context of the published structural information on coproheme-bound and MMD-bound coproheme decarboxylase and with respect to the reaction mechanism. Having structural information of all four enzymatically relevant states helps in understanding structural restraints with a functional impact.
History
DepositionOct 19, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18688.png

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Map

FileDownload / File: emd_18688.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 360.288 Å		0.83 Å/pix.
x 432 pix.
= 360.288 Å		0.83 Å/pix.
x 432 pix.
= 360.288 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.29913756 - 0.5899389
Average (Standard dev.)-0.00010519479 (±0.010180312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 358.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18688_half_map_1.map
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Half map: #1

Fileemd_18688_half_map_2.map
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Sample components

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Entire : Structure of Apo coproheme decarboxylase from Corynebacterium dip...

EntireName: Structure of Apo coproheme decarboxylase from Corynebacterium diphtheria
Components
  • Complex: Structure of Apo coproheme decarboxylase from Corynebacterium diphtheria
    • Protein or peptide: Coproheme decarboxylase
  • Ligand: water

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Supramolecule #1: Structure of Apo coproheme decarboxylase from Corynebacterium dip...

SupramoleculeName: Structure of Apo coproheme decarboxylase from Corynebacterium diphtheria
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Corynebacterium diphtheriae (bacteria)
Molecular weightTheoretical: 136.3 kDa/nm

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Macromolecule #1: Coproheme decarboxylase

MacromoleculeName: Coproheme decarboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium diphtheriae (bacteria)
Molecular weightTheoretical: 27.288961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPMAEKLNFE ELNSMQRYSQ FAVFRAIPGA LGSDRAEIVA QAQSFFDGLE TAGKVEVRGI YDLAGCRAEA DFMIWWIAEE FEEIQAAFA RFRRETVLGQ VSEVAWLGNS LHRPAEFNRS HLPSFIMGEI PGDWITVYPF VRSYDWYIMD PQKRRKILAE H GQAARDFP ...String:
GPMAEKLNFE ELNSMQRYSQ FAVFRAIPGA LGSDRAEIVA QAQSFFDGLE TAGKVEVRGI YDLAGCRAEA DFMIWWIAEE FEEIQAAFA RFRRETVLGQ VSEVAWLGNS LHRPAEFNRS HLPSFIMGEI PGDWITVYPF VRSYDWYIMD PQKRRKILAE H GQAARDFP DVRANTVPAF ALGDYEWMLA FEAPRLDRIV DLMHKMRYTE ARLHVREETP FFTGRRVSEV SELVNVLPG

UniProtKB: Coproheme decarboxylase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 306 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration18 mg/mL
BufferpH: 7.5 / Component - Formula: NaCl / Component - Name: Sodium Chloride / Details: 100mM Phosphate Buffer
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Pressure: 0.03 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Blotting time; 5.0-5.5 sec. Blotting force; 18 or 19..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 1035 / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xuc

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 638556
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6xuc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8qwc:
Cryo-EM structure of Apo coproheme decarboxylase from Corynebacterium diphtheria.

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