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- EMDB-16433: Cryo-EM structure of NADH bound SLA dehydrogenase RlGabD from Rhi... -

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Basic information

Entry
Database: EMDB / ID: EMD-16433
TitleCryo-EM structure of NADH bound SLA dehydrogenase RlGabD from Rhizobium leguminosarum bv. trifolii SRD1565
Map dataPostprocess map
Sample
  • Complex: Tetrameric assembly of RlGabD
    • Protein or peptide: Succinate semialdehyde dehydrogenase
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: water
KeywordsSulfolactaldehyde dehydrogenase NADH GabD / OXIDOREDUCTASE
Biological speciesRhizobium leguminosarum bv. trifolii SRDI565 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsSharma M / Meek RW / Armstrong Z / Blaza JN / Alhifthi A / Li J / Goddard-Borger ED / Williams SJ / Davies GJ
Funding support United Kingdom, Australia, 6 items
OrganizationGrant numberCountry
Royal SocietyRP/EA/180016 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
National Health and Medical Research Council (NHMRC, Australia)GNT2000517 Australia
The Walter and Eliza Hall Institute of Medical Research Australia
The Australian Cancer Research Fund Australia
The Brian M. Davis Charitable Foundation Centenary Fellowship Australia
CitationJournal: Chem Sci / Year: 2023
Title: Molecular basis of sulfolactate synthesis by sulfolactaldehyde dehydrogenase from .
Authors: Jinling Li / Mahima Sharma / Richard Meek / Amani Alhifthi / Zachary Armstrong / Niccolay Madiedo Soler / Mihwa Lee / Ethan D Goddard-Borger / James N Blaza / Gideon J Davies / Spencer J Williams /
Abstract: Sulfolactate (SL) is a short-chain organosulfonate that is an important reservoir of sulfur in the biosphere. SL is produced by oxidation of sulfolactaldehyde (SLA), which in turn derives from ...Sulfolactate (SL) is a short-chain organosulfonate that is an important reservoir of sulfur in the biosphere. SL is produced by oxidation of sulfolactaldehyde (SLA), which in turn derives from sulfoglycolysis of the sulfosugar sulfoquinovose, or through oxidation of 2,3-dihydroxypropanesulfonate. Oxidation of SLA is catalyzed by SLA dehydrogenases belonging to the aldehyde dehydrogenase superfamily. We report that SLA dehydrogenase GabD from the sulfoglycolytic bacterium SRDI565 can use both NAD and NADP as cofactor to oxidize SLA, and indicatively operates through a rapid equilibrium ordered mechanism. We report the cryo-EM structure of GabD bound to NADH, revealing a tetrameric quaternary structure and supporting proposal of organosulfonate binding residues in the active site, and a catalytic mechanism. Sequence based homology searches identified SLA dehydrogenase homologs in a range of putative sulfoglycolytic gene clusters in bacteria predominantly from the phyla Actinobacteria, Firmicutes, and Proteobacteria. This work provides a structural and biochemical view of SLA dehydrogenases to complement our knowledge of SLA reductases, and provide detailed insights into a critical step in the organosulfur cycle.
History
DepositionJan 6, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16433.png

Downloads & links

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Map

FileDownload / File: emd_16433.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocess map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 257.152 Å		1 Å/pix.
x 256 pix.
= 257.152 Å		1 Å/pix.
x 256 pix.
= 257.152 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0045 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.14261316 - 0.2378539
Average (Standard dev.)-0.000007917815 (±0.008815544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 257.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16433_msk_1.map
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Half map: HalfMap2

Fileemd_16433_half_map_1.map
AnnotationHalfMap2
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Half map: HalfMap1

Fileemd_16433_half_map_2.map
AnnotationHalfMap1
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Sample components

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Entire : Tetrameric assembly of RlGabD

EntireName: Tetrameric assembly of RlGabD
Components
  • Complex: Tetrameric assembly of RlGabD
    • Protein or peptide: Succinate semialdehyde dehydrogenase
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Tetrameric assembly of RlGabD

SupramoleculeName: Tetrameric assembly of RlGabD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhizobium leguminosarum bv. trifolii SRDI565 (bacteria)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Succinate semialdehyde dehydrogenase

MacromoleculeName: Succinate semialdehyde dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rhizobium leguminosarum bv. trifolii SRDI565 (bacteria)
Molecular weightTheoretical: 52.697355 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTERRTLALK DPALLTDKAF VAGAWIGAPD GKSIAVTDPF DGALIANVPD LGQAVVAQAI DAAAEAQKLW ERRTAKERAQ VLKRWYDLI VENADDLALI LTTEQGKPLA EARGEVVSNA AYLEWFAEEA KRIDGDIIPG PNAGQRIMVL KQPVGVCAAI T PWNFPNGM ...String:
MTERRTLALK DPALLTDKAF VAGAWIGAPD GKSIAVTDPF DGALIANVPD LGQAVVAQAI DAAAEAQKLW ERRTAKERAQ VLKRWYDLI VENADDLALI LTTEQGKPLA EARGEVVSNA AYLEWFAEEA KRIDGDIIPG PNAGQRIMVL KQPVGVCAAI T PWNFPNGM ITRKAGPALA AGCSMILKPA SQTPLSALAL AVLAERAGVP KGVFSVVTGE AKPIGLEFCH NPRIAKITFT GS TGVGRWL MKEAAGGIKR LSLELGGNAP FIVFDDADLD AAVEGAMISK FRNAGQTCVC ANRIYVQESV AAAFTERLLA KVS GLSLGR GTDAGVSQGP LIDEKAVAKM EEHIADAMAN GGTVLTGGKR SVLGGTFFEP TVVTGVTQTM KVAKEETFAP LAPI ISFKH ENDVIAMAND SEFGLASYFY AKDMARIWRV AEALEAGMVG VNTGMIANEM APFGGIKQSG TGREGSKYGI EGFLE LKYV ALGGMLEHHH HHH

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Macromolecule #2: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 330 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 50mM Tris, 300mM NaCl, pH7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 240000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Particle selectionNumber selected: 437107
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 75165
FSC plot (resolution estimation)

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