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- PDB-29to: Structure of monomerized and de-glycosylated native leukocyte mye... -

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Basic information

Entry
Database: PDB / ID: 29to
TitleStructure of monomerized and de-glycosylated native leukocyte myeloperoxidase in complex with the Staphylococcal Peroxidase Inhibitor SPIN
Components
  • (Myeloperoxidase ...) x 2
  • Myeloperoxidase
KeywordsOXIDOREDUCTASE / Innate immunity / homodimer / inhibitor
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / neutrophil-mediated killing of symbiont cell / myeloperoxidase / positive regulation of cholesterol import / neutrophil extracellular trap / phagocytic vesicle lumen / neutrophil-mediated killing of bacterium / cytolytic granule / response to gold nanoparticle / peroxidase inhibitor activity ...Events associated with phagocytolytic activity of PMN cells / neutrophil-mediated killing of symbiont cell / myeloperoxidase / positive regulation of cholesterol import / neutrophil extracellular trap / phagocytic vesicle lumen / neutrophil-mediated killing of bacterium / cytolytic granule / response to gold nanoparticle / peroxidase inhibitor activity / thiocyanate peroxidase activity / neutrophil extracellular trap formation / neutrophil-mediated killing of fungus / protein-containing complex destabilizing activity / symbiont-mediated evasion of host immune response / low-density lipoprotein particle remodeling / host cell cytoplasmic vesicle / nucleosome disassembly / azurophil granule / response to food / response to mechanical stimulus / phagocytic vesicle / nucleosome binding / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to lipopolysaccharide / response to oxidative stress / defense response to bacterium / lysosome / chromosome / chromatin binding / heme binding / negative regulation of apoptotic process / Neutrophil degranulation / extracellular exosome / extracellular region / nucleus
Similarity search - Function
: / Lactoperoxidase-like, N-terminal domain / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Myeloperoxidase / Myeloperoxidase inhibitor SPIN
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsLeitgeb, U. / Pfanzagl, V.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP33997 Austria
Austrian Science FundW1224 Austria
CitationJournal: Int J Biol Macromol / Year: 2026
Title: Interface N-glycans drive myeloperoxidase dimerization in vitro.
Authors: Urban Leitgeb / Yirui Guo / Tabitha Emde / Valentina Ruocco / Theodor Simak / Ela Zdenkovic / Paul G Furtmüller / Dominika Borek / William M Nauseef / Chris Oostenbrink / Vera Pfanzagl /
Abstract: Myeloperoxidase (MPO) is a highly glycosylated heme oxidoreductase that, together with lactoperoxidase (LPO) and eosinophil peroxidase (EPO), contributes to host defence through the generation of ...Myeloperoxidase (MPO) is a highly glycosylated heme oxidoreductase that, together with lactoperoxidase (LPO) and eosinophil peroxidase (EPO), contributes to host defence through the generation of (pseudo)hypohalous acids. Among the human heme peroxidases, mature MPO forms a unique covalently linked homodimer. Dimerization enhances stability and is essential for some biological functions, including chromatin disruption during neutrophil extracellular trap formation. Thus, we hypothesized that MPO dimerization must reflect a tightly regulated step in MPO biosynthesis and is driven by specific structural elements. Cross-species sequence alignment indicated that N-glycosylation motifs were evolutionarily more conserved in MPO than in monomeric EPO and LPO. We investigated the role of N-glycans in MPO dimerization using in vitro monomerized glycosylated (mMPO) and deglycosylated (mMPOdg) monomeric variants of native human MPO. Small-angle X-ray scattering, isothermal titration calorimetry and crystal structures showed that glycosylated MPO monomers had a weak but biologically relevant affinity in the millimolar range, which was lost upon deglycosylation. Furthermore, we present the first cryogenic transmission electron microscopy structure of human MPO with at least one core N-acetylglucosamine residue resolved at each N-glycosylation site. Structural analysis suggests that an extensive hydrogen bonding network of interface N-glycans at position 483 and residues of the other monomer drives MPO homodimerization. Dimerization enhances stability without affecting enzymatic activity. Together, we show that N-glycans are essential to MPO dimerization, provide important insights into the impact of interface N-glycans on biophysical and biochemical properties of MPO and discuss the implications for the biological roles of MPO in health and disease.
History
DepositionApr 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase light chain
B: Myeloperoxidase
C: Myeloperoxidase inhibitor SPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,43719
Polymers74,6673
Non-polymers1,77016
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18080 Å2
ΔGint-193 kcal/mol
Surface area24060 Å2
Unit cell
Length a, b, c (Å)56.819, 84.075, 128.637
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Myeloperoxidase ... , 2 types, 2 molecules AC

#1: Protein Myeloperoxidase light chain


Mass: 12894.465 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 167-271 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P05164
#3: Protein Myeloperoxidase inhibitor SPIN


Mass: 8394.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAOUHSC_00401 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G0X2

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Protein / Sugars , 2 types, 4 molecules B

#2: Protein Myeloperoxidase / MPO


Mass: 53378.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P05164, myeloperoxidase
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 533 molecules

#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2 20% PEG3350

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Data collection

DiffractionMean temperature: 213 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Feb 26, 2025 / Details: ELLIPTICAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.437→70.377 Å / Num. obs: 87698 / % possible obs: 93.4 % / Redundancy: 9.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.275 / Rpim(I) all: 0.094 / Rrim(I) all: 0.291 / Net I/σ(I): 7.4
Reflection shellResolution: 1.437→1.572 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.519 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4385 / CC1/2: 0.277 / Rpim(I) all: 0.813 / Rrim(I) all: 2.65 / % possible all: 49.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.126)refinement
Aimless0.8.2data scaling
gemmi0.7.3data extraction
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→70.377 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.128 / SU B: 4.067 / SU ML: 0.063 / Average fsc free: 0.9688 / Average fsc work: 0.9818 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 4408 5.026 %RANDOM
Rwork0.1398 83288 --
all0.143 ---
obs-87696 78.233 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.639 Å20 Å2-0 Å2
2---0.751 Å20 Å2
3---0.112 Å2
Refinement stepCycle: LAST / Resolution: 1.44→70.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 103 520 5684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125350
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165062
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.8487279
X-RAY DIFFRACTIONr_angle_other_deg0.6831.77211613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.231569
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.53352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35710901
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.8610264
X-RAY DIFFRACTIONr_chiral_restr0.10.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021340
X-RAY DIFFRACTIONr_nbd_refined0.230.21006
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24579
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22596
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2305
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.222
X-RAY DIFFRACTIONr_nbd_other0.2020.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.225
X-RAY DIFFRACTIONr_mcbond_it5.1431.2062530
X-RAY DIFFRACTIONr_mcbond_other5.141.2052530
X-RAY DIFFRACTIONr_mcangle_it7.5712.1743160
X-RAY DIFFRACTIONr_mcangle_other7.5732.1743161
X-RAY DIFFRACTIONr_scbond_it7.5091.4892820
X-RAY DIFFRACTIONr_scbond_other7.51.4892819
X-RAY DIFFRACTIONr_scangle_it10.5892.6124110
X-RAY DIFFRACTIONr_scangle_other10.5872.6124111
X-RAY DIFFRACTIONr_lrange_it13.85415.0756027
X-RAY DIFFRACTIONr_lrange_other13.23614.2085932
X-RAY DIFFRACTIONr_rigid_bond_restr4.272310412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.44-1.4770.29980.2731080.27581870.9690.9391.41690.259
1.477-1.5180.28390.2796760.27979940.9420.948.94420.271
1.518-1.5620.3181120.2625140.26277750.9330.9533.77490.251
1.562-1.610.32590.24247450.24475470.9360.95866.30450.23
1.61-1.6630.283270.23459650.23673400.9450.96285.72210.216
1.663-1.7210.2673250.21265370.21571110.9530.96996.49840.19
1.721-1.7860.2433420.18664990.18968440.960.97799.95620.161
1.786-1.8590.2133140.15562630.15865800.9710.98499.95440.13
1.859-1.9410.2063010.13360460.13763480.9740.98899.98420.109
1.941-2.0360.1833090.12157720.12460830.9770.9999.96710.101
2.036-2.1460.183230.11354490.11657730.980.99299.98270.097
2.146-2.2760.1672820.1152260.11355080.9810.9931000.097
2.276-2.4330.1862770.10448540.10951310.9790.9931000.094
2.433-2.6280.1632210.10645890.10948100.9830.9931000.098
2.628-2.8780.1762230.11642520.11944760.980.99199.97770.11
2.878-3.2170.1912090.12738330.1340460.9790.9999.90110.125
3.217-3.7140.1741770.11334040.11635820.9810.99299.97210.117
3.714-4.5450.1511690.11629070.11830780.9870.99299.9350.125
4.545-6.4140.21270.16222980.16524250.9860.9891000.173
6.414-70.3770.228640.20313510.20414220.9690.96699.50770.225

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