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- PDB-9q2u: Crystal structure of lactate racemase A with a single catalytic h... -

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Basic information

Entry
Database: PDB / ID: 9q2u
TitleCrystal structure of lactate racemase A with a single catalytic histidine from Streptococcus plurextorum
ComponentsLactate racemase A
KeywordsISOMERASE / Racemase and epimerase activity / acting on hydroxy acids and derivatives / metal ion binding / catalytic activity
Biological speciesStreptococcus plurextorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsGatreddi, S. / Hausinger, R.P. / Hu, J.
Funding support United States, 2items
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)GM128959 United States
CitationJournal: Protein Sci / 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 / Benoît 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 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactate racemase A
B: Lactate racemase A


Theoretical massNumber of molelcules
Total (without water)112,6792
Polymers112,6792
Non-polymers00
Water37821
1
B: Lactate racemase A

B: Lactate racemase A

B: Lactate racemase A

B: Lactate racemase A

A: Lactate racemase A

A: Lactate racemase A

A: Lactate racemase A

A: Lactate racemase A


Theoretical massNumber of molelcules
Total (without water)450,7158
Polymers450,7158
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_555x+1/2,y+1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-y+1/2,x+1/2,z+1/21
crystal symmetry operation8_555y+1/2,-x+1/2,z+1/21
Unit cell
Length a, b, c (Å)145.224, 145.224, 116.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Lactate racemase A


Mass: 56339.324 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.49 M Sodium phosphate monobasic monohydrate and 0.91 M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.108→34.23 Å / Num. obs: 21937 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.326 / Rpim(I) all: 0.09 / Rrim(I) all: 0.338 / Net I/σ(I): 7.3
Reflection shellResolution: 3.108→3.161 Å / Rmerge(I) obs: 4.635 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1077 / CC1/2: 0.364 / Rpim(I) all: 1.244 / Rrim(I) all: 4.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→34.23 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2824 1069 4.89 %
Rwork0.2227 --
obs0.2256 21937 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7159 0 0 21 7180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127346
X-RAY DIFFRACTIONf_angle_d1.4489981
X-RAY DIFFRACTIONf_dihedral_angle_d7.4551005
X-RAY DIFFRACTIONf_chiral_restr0.0751087
X-RAY DIFFRACTIONf_plane_restr0.0121308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.250.40221170.34472568X-RAY DIFFRACTION99
3.25-3.420.36611460.28812577X-RAY DIFFRACTION100
3.42-3.630.32241220.27822604X-RAY DIFFRACTION100
3.63-3.910.36821360.28012590X-RAY DIFFRACTION99
3.91-4.310.27141310.22832597X-RAY DIFFRACTION100
4.31-4.930.2111300.18782624X-RAY DIFFRACTION100
4.93-6.20.25451620.21672586X-RAY DIFFRACTION100
6.21-34.230.2741250.17722663X-RAY DIFFRACTION100

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