4DL1

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Deconstruction of activity-dependent covalent modification of heme in human neutrophil myeloperoxidase by multistage mass spectrometry (MS(4)).

Geoghegan, K.F.Varghese, A.H.Feng, X.Bessire, A.J.Conboy, J.J.Ruggeri, R.B.Ahn, K.Spath, S.N.Filippov, S.V.Conrad, S.J.Carpino, P.A.Guimaraes, C.R.Vajdos, F.F.

(2012) Biochemistry 51: 2065-2077

  • DOI: 10.1021/bi201872j

  • PubMed Abstract: 
  • Myeloperoxidase (MPO) is known to be inactivated and covalently modified by treatment with hydrogen peroxide and agents similar to 3-(2-ethoxypropyl)-2-thioxo-2,3-dihydro-1H-purin-6(9H)-one (1), a 254.08 Da derivative of 2-thioxanthine. Peptide mappi ...

    Myeloperoxidase (MPO) is known to be inactivated and covalently modified by treatment with hydrogen peroxide and agents similar to 3-(2-ethoxypropyl)-2-thioxo-2,3-dihydro-1H-purin-6(9H)-one (1), a 254.08 Da derivative of 2-thioxanthine. Peptide mapping by liquid chromatography and mass spectrometry detected modification by 1 in a labile peptide-heme-peptide fragment of the enzyme, accompanied by a mass increase of 252.08 Da. The loss of two hydrogen atoms was consistent with mechanism-based oxidative coupling. Multistage mass spectrometry (MS(4)) of the modified fragment in an ion trap/Orbitrap spectrometer demonstrated that 1 was coupled directly to heme. Use of a 10 amu window delivered the full isotopic envelope of each precursor ion to collision-induced dissociation, preserving definitive isotopic profiles for iron-containing fragments through successive steps of multistage mass spectrometry. Iron isotope signatures and accurate mass measurements supported the structural assignments. Crystallographic analysis confirmed linkage between the methyl substituent of the heme pyrrole D ring and the sulfur atom of 1. The final orientation of 1 perpendicular to the plane of the heme ring suggested a mechanism consisting of two consecutive one-electron oxidations of 1 by MPO. Multistage mass spectrometry using stage-specific collision energies permits stepwise deconstruction of modifications of heme enzymes containing covalent links between the heme group and the polypeptide chain.


    Organizational Affiliation

    Pfizer Worldwide Research, Groton, Connecticut 06340, United States. kieran.f.geoghegan@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myeloperoxidase light chain
A, B, E, F, I, J, M, N
104Homo sapiensMutation(s): 0 
Gene Names: MPO
EC: 1.11.2.2
Find proteins for P05164 (Homo sapiens)
Go to Gene View: MPO
Go to UniProtKB:  P05164
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Myeloperoxidase heavy chain
C, D, G, H, K, L, O, P
466Homo sapiensMutation(s): 0 
Gene Names: MPO
EC: 1.11.2.2
Find proteins for P05164 (Homo sapiens)
Go to Gene View: MPO
Go to UniProtKB:  P05164
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A, B, E, F, I, J, M, N
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
C, D, G, H, K, L, O, P
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
C, D, G, H, K, L, O, P
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
0KY
Query on 0KY

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Download CCD File 
A, B, G, H, I, J, O, P
3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one
C10 H14 N4 O2 S
QOTIDWBGIWZLOV-ZCFIWIBFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
C, D, G, H, K, L, O, P
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
C, D, G, H, K, L, O, P
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
B, C, E, F, I, J, M, N
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
C, D, G, H, K, L, O, P
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
C, D, G, H, K, L, O, P
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.829α = 90.00
b = 242.636β = 91.19
c = 151.505γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-09
    Type: Database references