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- EMDB-72200: Structure of LarA-like nickel-pincer nucleotide cofactor-utilizin... -

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Basic information

Entry
Database: EMDB / ID: EMD-72200
TitleStructure of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Streptococcus plurextorum
Map data
Sample
  • Complex: Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
    • Protein or peptide: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
  • Ligand: NICKEL (II) ION
  • Ligand: 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium
KeywordsRacemase and epimerase activity / acting on hydroxy acids and derivatives / metal ion binding / catalytic activity / ISOMERASE
Biological speciesStreptococcus plurextorum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSubramanian S / Gatreddi S / Hausinger RP / Hu J / Parent KN
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140931 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
CitationJournal: bioRxiv / Year: 2025
Title: Structures of two LarA-like nickel-pincer nucleotide cofactor-utilizing enzymes with a single catalytic histidine residue.
Authors: Santhosh Gatreddi / Sundharraman Subramanian / Dexin Sui / Tianqi Wang / Julian Urdiain-Arraiza / Benoit Desguin / Robert P Hausinger / Kristin N Parent / Jian Hu /
Abstract: The nickel pincer nucleotide (NPN) cofactor catalyzes the racemization/epimerization of α-hydroxy acids in enzymes of the LarA family. The established proton-coupled hydride transfer mechanism ...The nickel pincer nucleotide (NPN) cofactor catalyzes the racemization/epimerization of α-hydroxy acids in enzymes of the LarA family. The established proton-coupled hydride transfer mechanism requires two catalytic histidine residues that alternately act as general acids and general bases. Notably, however, a fraction of LarA homologs (LarAHs) lack one of the active site histidine residues, replacing it with an asparaginyl side chain that cannot participate in acid/base catalysis. Here, we investigated two such LarAHs and solved their cryo-electron microscopic structures with and without loaded NPN cofactor, respectively. The structures revealed a consistent octameric assembly that is unprecedented in the LarA family and unveiled a new set of active site residues that likely recognize and process substrates differently from those of the well-studied LarAHs. Genomic context analysis suggested their potential involvement in carbohydrate metabolism. Together, these findings lay the groundwork for expanding the breadth of reactions and the range of mechanisms of LarA enzymes.
History
DepositionAug 18, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72200.png

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Map

FileDownload / File: emd_72200.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 300 pix.
= 265.8 Å		0.89 Å/pix.
x 300 pix.
= 265.8 Å		0.89 Å/pix.
x 300 pix.
= 265.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.886 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.7263951 - 1.063828
Average (Standard dev.)0.00068179163 (±0.03252784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 265.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72200_msk_1.map
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Half map: #2

Fileemd_72200_half_map_1.map
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Half map: #1

Fileemd_72200_half_map_2.map
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Sample components

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Entire : Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme

EntireName: Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
Components
  • Complex: Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
    • Protein or peptide: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
  • Ligand: NICKEL (II) ION
  • Ligand: 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium

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Supramolecule #1: Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme

SupramoleculeName: Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptococcus plurextorum (bacteria)

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Macromolecule #1: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme

MacromoleculeName: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus plurextorum (bacteria)
Molecular weightTheoretical: 56.339324 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString: MKIDFEYGHG TMTADLPDTT DIFIPGETVA DPECLPEDQI EAATLDSIRN PLGMPPLTEL AKPGSKVTIV FPDRVKGGEQ ATAHRKVSI KLILQELYSV GVKKEDILLI CSNGLHRKNT EKEILGVLGP DLYHQFAPTG QIINHDSEDY EHLVDLGKTK Q GDPVIMNK ...String:
MKIDFEYGHG TMTADLPDTT DIFIPGETVA DPECLPEDQI EAATLDSIRN PLGMPPLTEL AKPGSKVTIV FPDRVKGGEQ ATAHRKVSI KLILQELYSV GVKKEDILLI CSNGLHRKNT EKEILGVLGP DLYHQFAPTG QIINHDSEDY EHLVDLGKTK Q GDPVIMNK YVYESDVAIL IGHTQGNPYG GYSGGYKHCS TGITHWKSIA SHHVPKVMHR KDFVPVNNNS LMRHKFDEIG MH MEEKMGK KFFCCDAVLD TKSRQIEINS GAADEVQKKA WKLGNARTYV PFAEKKYDII VFGMPQFFHY GDGMGTNPIM LMQ ALSAQV IRHKRIMSDN CVFICASTCN GYFNESLWPY LPELYDLFQK EGNTLVDLNQ YGEYFATNEE YIRKYRYAHA FHPF HGFSM ISCAHLAEKH TAAIYLVGAE KPGYARGMGL KTRATFEEAL EDAKKKFVGQ EPNILALPKA FKTAAVHLMM KNDLP PMTP RYEENHWSHP QFEK

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Macromolecule #2: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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Macromolecule #3: 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfany...

MacromoleculeName: 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium
type: ligand / ID: 3 / Number of copies: 8 / Formula: 4EY
Molecular weightTheoretical: 396.353 Da

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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

Concentration1.5 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO32-Amino-2-hydroxymethyl-propane-1,3-diol
125.0 mMNaClSodium Chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3949 / Average electron dose: 44.71 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Ab-initio reconstructions were used to generate the initial model
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 571000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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