4DL1

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog

PDB DOI: https://doi.org/10.2210/pdb4DL1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2012-02-05 Released: 2012-03-21
Deposition Author(s): Vajdos, F., Varghese, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.246
R-Value Work: 0.190
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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

PubMed: 22352991 Search on PubMed
DOI: https://doi.org/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 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

Macromolecule Content

Total Structure Weight: 541.36 kDa
Atom Count: 40,392
Modelled Residue Count: 4,557
Deposited Residue Count: 4,560
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase light chain	A C [auth B] E G [auth F] I A, C [auth B], E, G [auth F], I, K [auth J], M, O [auth N]	104	Homo sapiens	Mutation(s): 0 EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens) Explore P05164 Go to UniProtKB: P05164
PHAROS: P05164 GTEx: ENSG00000005381
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05164
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase heavy chain	B [auth C] D F [auth G] H J [auth K] B [auth C], D, F [auth G], H, J [auth K], L, N [auth O], P	466	Homo sapiens	Mutation(s): 0 EC: 1.11.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P05164 (Homo sapiens) Explore P05164 Go to UniProtKB: P05164
PHAROS: P05164 GTEx: ENSG00000005381
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05164
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B [auth C] Focus chain D Focus chain F [auth G] Focus chain H Focus chain J [auth K] Focus chain L Focus chain N [auth O] Focus chain P	Go to GlyGen: P05164-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	Q, R, S, T, U Q, R, S, T, U, V, W, X	6		N-Glycosylation	Interactions Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Y	5		N-Glycosylation	Interactions Focus chain Y Interactions & Density Focus chain Y
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain EB [auth J] SDF format, chain GA [auth B] SDF format, chain KB [auth M] SDF format, chain MA [auth E] SDF format, chain QB [auth N] SDF format, chain SA [auth F] SDF format, chain YA [auth I] SDF format, chain BA [auth C] MOL2 format, chain EB [auth J] MOL2 format, chain GA [auth B] MOL2 format, chain KB [auth M] MOL2 format, chain MA [auth E] MOL2 format, chain QB [auth N] MOL2 format, chain SA [auth F] MOL2 format, chain YA [auth I] MOL2 format, chain BA [auth C] mmCIF format, chain EB [auth J] mmCIF format, chain GA [auth B] mmCIF format, chain KB [auth M] mmCIF format, chain MA [auth E] mmCIF format, chain QB [auth N] mmCIF format, chain SA [auth F] mmCIF format, chain YA [auth I] mmCIF format, chain BA [auth C]	BA [auth C] EB [auth J] GA [auth B] KB [auth M] MA [auth E] BA [auth C], EB [auth J], GA [auth B], KB [auth M], MA [auth E], QB [auth N], SA [auth F], YA [auth I]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth C] Focus chain EB [auth J] Focus chain GA [auth B] Focus chain KB [auth M] Focus chain MA [auth E] Focus chain QB [auth N] Focus chain SA [auth F] Focus chain YA [auth I] Interactions & Density Focus chain BA [auth C] Focus chain EB [auth J] Focus chain GA [auth B] Focus chain KB [auth M] Focus chain MA [auth E] Focus chain QB [auth N] Focus chain SA [auth F] Focus chain YA [auth I]
0KY Query on 0KY Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain FB [auth J] SDF format, chain HA [auth B] SDF format, chain OB [auth O] SDF format, chain QA [auth G] SDF format, chain TB [auth P] SDF format, chain WA [auth H] SDF format, chain ZA [auth I] MOL2 format, chain AA [auth A] MOL2 format, chain FB [auth J] MOL2 format, chain HA [auth B] MOL2 format, chain OB [auth O] MOL2 format, chain QA [auth G] MOL2 format, chain TB [auth P] MOL2 format, chain WA [auth H] MOL2 format, chain ZA [auth I] mmCIF format, chain AA [auth A] mmCIF format, chain FB [auth J] mmCIF format, chain HA [auth B] mmCIF format, chain OB [auth O] mmCIF format, chain QA [auth G] mmCIF format, chain TB [auth P] mmCIF format, chain WA [auth H] mmCIF format, chain ZA [auth I]	AA [auth A] FB [auth J] HA [auth B] OB [auth O] QA [auth G] AA [auth A], FB [auth J], HA [auth B], OB [auth O], QA [auth G], TB [auth P], WA [auth H], ZA [auth I]	3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one C₁₀ H₁₄ N₄ O₂ S QOTIDWBGIWZLOV-ZCFIWIBFSA-N		Interactions Focus chain AA [auth A] Focus chain FB [auth J] Focus chain HA [auth B] Focus chain OB [auth O] Focus chain QA [auth G] Focus chain TB [auth P] Focus chain WA [auth H] Focus chain ZA [auth I] Interactions & Density Focus chain AA [auth A] Focus chain FB [auth J] Focus chain HA [auth B] Focus chain OB [auth O] Focus chain QA [auth G] Focus chain TB [auth P] Focus chain WA [auth H] Focus chain ZA [auth I]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BB [auth K] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain GB [auth L] SDF format, chain HB [auth L] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain LB [auth O] SDF format, chain MB [auth O] SDF format, chain NA [auth G] SDF format, chain OA [auth G] SDF format, chain SB [auth P] SDF format, chain TA [auth H] SDF format, chain UA [auth H] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth K] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain GB [auth L] MOL2 format, chain HB [auth L] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain LB [auth O] MOL2 format, chain MB [auth O] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain SB [auth P] MOL2 format, chain TA [auth H] MOL2 format, chain UA [auth H] mmCIF format, chain AB [auth K] mmCIF format, chain BB [auth K] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain GB [auth L] mmCIF format, chain HB [auth L] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain LB [auth O] mmCIF format, chain MB [auth O] mmCIF format, chain NA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain SB [auth P] mmCIF format, chain TA [auth H] mmCIF format, chain UA [auth H]	AB [auth K] BB [auth K] CA [auth C] DA [auth C] GB [auth L] AB [auth K], BB [auth K], CA [auth C], DA [auth C], GB [auth L], HB [auth L], IA [auth D], JA [auth D], LB [auth O], MB [auth O], NA [auth G], OA [auth G], SB [auth P], TA [auth H], UA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain GB [auth L] Focus chain HB [auth L] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain LB [auth O] Focus chain MB [auth O] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain SB [auth P] Focus chain TA [auth H] Focus chain UA [auth H] Interactions & Density Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain GB [auth L] Focus chain HB [auth L] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain LB [auth O] Focus chain MB [auth O] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain SB [auth P] Focus chain TA [auth H] Focus chain UA [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CB [auth K] SDF format, chain EA [auth C] SDF format, chain IB [auth L] SDF format, chain KA [auth D] SDF format, chain NB [auth O] SDF format, chain PA [auth G] SDF format, chain RB [auth P] SDF format, chain VA [auth H] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth C] MOL2 format, chain IB [auth L] MOL2 format, chain KA [auth D] MOL2 format, chain NB [auth O] MOL2 format, chain PA [auth G] MOL2 format, chain RB [auth P] MOL2 format, chain VA [auth H] mmCIF format, chain CB [auth K] mmCIF format, chain EA [auth C] mmCIF format, chain IB [auth L] mmCIF format, chain KA [auth D] mmCIF format, chain NB [auth O] mmCIF format, chain PA [auth G] mmCIF format, chain RB [auth P] mmCIF format, chain VA [auth H]	CB [auth K] EA [auth C] IB [auth L] KA [auth D] NB [auth O] CB [auth K], EA [auth C], IB [auth L], KA [auth D], NB [auth O], PA [auth G], RB [auth P], VA [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CB [auth K] Focus chain EA [auth C] Focus chain IB [auth L] Focus chain KA [auth D] Focus chain NB [auth O] Focus chain PA [auth G] Focus chain RB [auth P] Focus chain VA [auth H] Interactions & Density Focus chain CB [auth K] Focus chain EA [auth C] Focus chain IB [auth L] Focus chain KA [auth D] Focus chain NB [auth O] Focus chain PA [auth G] Focus chain RB [auth P] Focus chain VA [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DB [auth J] SDF format, chain FA [auth B] SDF format, chain JB [auth M] SDF format, chain LA [auth E] SDF format, chain PB [auth N] SDF format, chain RA [auth F] SDF format, chain XA [auth I] SDF format, chain Z [auth A] MOL2 format, chain DB [auth J] MOL2 format, chain FA [auth B] MOL2 format, chain JB [auth M] MOL2 format, chain LA [auth E] MOL2 format, chain PB [auth N] MOL2 format, chain RA [auth F] MOL2 format, chain XA [auth I] MOL2 format, chain Z [auth A] mmCIF format, chain DB [auth J] mmCIF format, chain FA [auth B] mmCIF format, chain JB [auth M] mmCIF format, chain LA [auth E] mmCIF format, chain PB [auth N] mmCIF format, chain RA [auth F] mmCIF format, chain XA [auth I] mmCIF format, chain Z [auth A]	DB [auth J] FA [auth B] JB [auth M] LA [auth E] PB [auth N] DB [auth J], FA [auth B], JB [auth M], LA [auth E], PB [auth N], RA [auth F], XA [auth I], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DB [auth J] Focus chain FA [auth B] Focus chain JB [auth M] Focus chain LA [auth E] Focus chain PB [auth N] Focus chain RA [auth F] Focus chain XA [auth I] Focus chain Z [auth A] Interactions & Density Focus chain DB [auth J] Focus chain FA [auth B] Focus chain JB [auth M] Focus chain LA [auth E] Focus chain PB [auth N] Focus chain RA [auth F] Focus chain XA [auth I] Focus chain Z [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B [auth C] D F [auth G] H J [auth K] B [auth C], D, F [auth G], H, J [auth K], L, N [auth O], P	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.246
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.829	α = 90
b = 242.636	β = 91.19
c = 151.505	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Vajdos, F.

Varghese, A.

Revision History (Full details and data files)

Version 1.0: 2012-03-21
Type: Initial release
Version 1.1: 2012-05-09
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary