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- PDB-9q3j: Structures of LarA-like nickel-pincer nucleotide cofactor-utilizi... -

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Basic information

Entry
Database: PDB / ID: 9q3j
TitleStructures of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Blautia wexlerae
ComponentsDUF2088 domain-containing protein
KeywordsISOMERASE / Racemase and epimerase activity / acting on hydroxy acids and derivatives / metal ion binding / catalytic activity
Function / homologylactate racemase activity / LarA-like, N-terminal / : / Lactate racemase N-terminal domain / DUF2088 domain-containing protein
Function and homology information
Biological speciesBlautia wexlerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 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 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF2088 domain-containing protein
B: DUF2088 domain-containing protein
C: DUF2088 domain-containing protein
D: DUF2088 domain-containing protein
E: DUF2088 domain-containing protein
F: DUF2088 domain-containing protein
G: DUF2088 domain-containing protein
H: DUF2088 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)460,0838
Polymers460,0838
Non-polymers00
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
DUF2088 domain-containing protein / Domain of uncharacterized function (DUF2088)


Mass: 57510.332 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blautia wexlerae (bacteria) / Gene: ERS852523_02626, GT728_05510 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0A174QNZ5
Has protein modificationN

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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: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Blautia wexlerae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-Gold(DE3)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
110.0 mMHEPESC8H18N2O4S1
2150.0 mMSodium ChlorideNaCl1
SpecimenConc.: 2 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: 120000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 32.27 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1415

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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: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219816 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00329609
ELECTRON MICROSCOPYf_angle_d0.53140006
ELECTRON MICROSCOPYf_dihedral_angle_d4.3023909
ELECTRON MICROSCOPYf_chiral_restr0.0434159
ELECTRON MICROSCOPYf_plane_restr0.0045189

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