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- EMDB-72199: Structures of LarA-like nickel-pincer nucleotide cofactor-utilizi... -

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Basic information

Entry
Database: EMDB / ID: EMD-72199
TitleStructures of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Blautia wexlerae
Map data
Sample
  • Complex: Apo LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
    • Protein or peptide: DUF2088 domain-containing protein
KeywordsRacemase and epimerase activity / acting on hydroxy acids and derivatives / metal ion binding / catalytic activity / ISOMERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 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 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72199.png

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Map

FileDownload / File: emd_72199.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261.6 Å		0.87 Å/pix.
x 300 pix.
= 261.6 Å		0.87 Å/pix.
x 300 pix.
= 261.6 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.872 Å
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Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.013353 - 4.341919
Average (Standard dev.)0.0043741036 (±0.15195341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72199_msk_1.map
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Half map: #2

Fileemd_72199_half_map_1.map
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Half map: #1

Fileemd_72199_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: DUF2088 domain-containing protein

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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: all
Source (natural)Organism: Blautia wexlerae (bacteria)

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Macromolecule #1: DUF2088 domain-containing protein

MacromoleculeName: DUF2088 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Blautia wexlerae (bacteria)
Molecular weightTheoretical: 57.510332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASKFDFEYG QGTMSAELPD NTDIFIPGET VKDPDHIPED QLEAAYLESL AHPIGMPTLT ELAGPGKTVT IVVPDRVKGG EQATSHRKL SIKYILKELY AAGVEKKDIL FIISNGLHPR STEADAKAIF GEELFNEFWH TGQIISHDSE DQEHMVDLGT T HRGDPVYM ...String:
MASKFDFEYG QGTMSAELPD NTDIFIPGET VKDPDHIPED QLEAAYLESL AHPIGMPTLT ELAGPGKTVT IVVPDRVKGG EQATSHRKL SIKYILKELY AAGVEKKDIL FIISNGLHPR STEADAKAIF GEELFNEFWH TGQIISHDSE DQEHMVDLGT T HRGDPVYM NKYVFECDIP ILIGHVQGNP YGGYSGGYKH SATGITNWKC IASHHVPSVM HRDDFTPVNG GSLMRNKFDE IS MHMEEKM GHPFFCCDAV LDTQSRQIAI YSGYAKEMMP ISWKLADKRT YVHWAEKKYD VLVFGMPQKF HYGDGMGTNP IMM MQALSA QVLRFKRVMS DNCVIICAST CNGYFHDERW PYLRELYDLF QHDHMNTLPD MNRLGEYFAT NEEYIRKYRY TNAF HPFHG FSMMSCGHIA EMNTSAIYIV GAEEPGYARG MGLKTRATFE EALEDAKKKY VGQEPNILAL PMTFKKAAVH LCMKD PAQD CMDEYGHRHP CCCLEHHHHH H

UniProtKB: DUF2088 domain-containing protein

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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

Concentration2 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
150.0 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 III (4k x 4k) / Number grids imaged: 1 / Number real images: 1415 / Average electron dose: 32.27 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: 120000
Sample stageSpecimen holder model: OTHER / 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 reconstruction were used to generate the initial model
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 219816
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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