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- PDB-9q3k: Structure of LarA-like nickel-pincer nucleotide cofactor-utilizin... -

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Basic information

Entry
Database: PDB / ID: 9q3k
TitleStructure of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Streptococcus plurextorum
ComponentsLarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
KeywordsISOMERASE / Racemase and epimerase activity / acting on hydroxy acids and derivatives / metal ion binding / catalytic activity
Function / homologyChem-4EY / NICKEL (II) ION
Function and homology information
Biological speciesStreptococcus plurextorum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSubramanian, S. / Gatreddi, S. / Hausinger, R.P. / Hu, J. / Parent, K.N.
Funding support United States, 3items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
D: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
A: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
H: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
E: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
F: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
C: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
G: LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,35524
Polymers450,7158
Non-polymers3,64016
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 56339.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus plurextorum (bacteria) / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ3900
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-4EY / 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium / Dithiodinicotinic acid mononucleotide


Mass: 396.353 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H15NO8PS2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Streptococcus plurextorum (bacteria)
Source (recombinant)Organism: Lactococcus lactis (lactic acid bacteria) / Strain: NZ3900
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
150.0 mM2-Amino-2-hydroxymethyl-propane-1,3-diolC4H11NO31
2125.0 mMSodium ChlorideNaCl1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44.71 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3949

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 571000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00331110
ELECTRON MICROSCOPYf_angle_d0.53742152
ELECTRON MICROSCOPYf_dihedral_angle_d6.9274210
ELECTRON MICROSCOPYf_chiral_restr0.0424524
ELECTRON MICROSCOPYf_plane_restr0.0055470

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