7Z53 | pdb_00007z53

Structure of native leukocyte myeloperoxidase in complex with a truncated version (SPIN truncated) of the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb7Z53/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens, Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-07 Released: 2022-10-26
Deposition Author(s): Pfanzagl, V., Brito, J.A.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.229 (Depositor), 0.228 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

Literature

The staphylococcal inhibitory protein SPIN binds to human myeloperoxidase with picomolar affinity but only dampens halide oxidation.

Leitgeb, U., Furtmuller, P.G., Hofbauer, S., Brito, J.A., Obinger, C., Pfanzagl, V.

(2022) J Biological Chem 298: 102514-102514

PubMed: 36150500 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2022.102514
Primary Citation Related Structures:
7QZR, 7Z53

PubMed Abstract:
The heme enzyme myeloperoxidase (MPO) is one of the key players in the neutrophil-mediated killing of invading pathogens as part of the innate immune system. MPO generates antimicrobial oxidants, which indiscriminately and effectively kill phagocytosed pathogens. Staphylococcus aureus, however, is able to escape this fate, in part by secreting a small protein called SPIN (Staphylococcal Peroxidase Inhibitor), which specifically targets and inhibits MPO in a structurally complex manner. Here, we present the first crystal structures of the complex of SPIN-aureus and a truncated version (SPIN-truncated) with mature dimeric leukocyte MPO. We unravel the contributions of the two domains to the kinetics and thermodynamics of SPIN-aureus binding to MPO by using a broad array of complementary biochemical and biophysical methods. The C-terminal "recognition" domain is shown to mediate specific binding to MPO, while interaction of the N-terminal "inhibitory" domain is guided mainly by hydrophobic effects and thus is less sequence dependent. We found that inhibition of MPO is achieved by reducing substrate migration, but SPIN-aureus cannot completely block MPO activity. Its' effectiveness is inversely related to substrate size, with no discernible dependence on other factors. Thus, SPIN-aureus is an extremely high-affinity inhibitor and highly efficient for substrates larger than halogens. As aberrant MPO activity is implicated in a number of chronic inflammatory diseases, SPIN-aureus is the first promising protein inhibitor for specific inhibition of human MPO.

Organizational Affiliation

University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Vienna, Austria.

Macromolecule Content

Total Structure Weight: 599.82 kDa
Atom Count: 42,796
Modeled Residue Count: 5,012
Deposited Residue Count: 5,048
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase light chain	A, C, G, I, M A, C, G, I, M, O, S, U	106	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05164
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase heavy chain	B, D, H, J, N B, D, H, J, N, P, T, V	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05164
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain D Focus chain H Focus chain J Focus chain N Focus chain P Focus chain T Focus chain V	Go to GlyGen: P05164-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase inhibitor SPIN	E, F, K, L, Q E, F, K, L, Q, R, W, X	59	Staphylococcus aureus	Mutation(s): 0 Gene Names: spn, KMZ21_01875
UniProt
Find proteins for Q2G0X2 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0X2 Go to UniProtKB: Q2G0X2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G0X2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f], LA [auth l], OA [auth o], RA [auth r], Y	3		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain LA [auth l] Focus chain OA [auth o] Focus chain RA [auth r] Focus chain Y Interactions & Density Focus chain FA [auth f] Focus chain LA [auth l] Focus chain OA [auth o] Focus chain RA [auth r] Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	Z	4		N-Glycosylation	Interactions Focus chain Z Interactions & Density Focus chain Z
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	AA [auth a], CA [auth c], EA [auth e], HA [auth h], KA [auth k], AA [auth a], CA [auth c], EA [auth e], HA [auth h], KA [auth k], NA [auth n], QA [auth q], TA [auth t]	6		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain KA [auth k] Focus chain NA [auth n] Focus chain QA [auth q] Focus chain TA [auth t] Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain KA [auth k] Focus chain NA [auth n] Focus chain QA [auth q] Focus chain TA [auth t]
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], DA [auth d], GA [auth g], MA [auth m], PA [auth p], BA [auth b], DA [auth d], GA [auth g], MA [auth m], PA [auth p], SA [auth s]	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain SA [auth s] Interactions & Density Focus chain BA [auth b] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	IA [auth i]	4		N-Glycosylation	Interactions Focus chain IA [auth i] Interactions & Density Focus chain IA [auth i]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	JA [auth j]	5		N-Glycosylation	Interactions Focus chain JA [auth j] Interactions & Density Focus chain JA [auth j]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain JB [auth I] SDF format, chain MB [auth M] SDF format, chain PB [auth O] SDF format, chain UB [auth S] SDF format, chain VA [auth A] SDF format, chain XB [auth U] SDF format, chain ZA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain JB [auth I] MOL2 format, chain MB [auth M] MOL2 format, chain PB [auth O] MOL2 format, chain UB [auth S] MOL2 format, chain VA [auth A] MOL2 format, chain XB [auth U] MOL2 format, chain ZA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain JB [auth I] mmCIF format, chain MB [auth M] mmCIF format, chain PB [auth O] mmCIF format, chain UB [auth S] mmCIF format, chain VA [auth A] mmCIF format, chain XB [auth U] mmCIF format, chain ZA [auth C]	FB [auth G] JB [auth I] MB [auth M] PB [auth O] UB [auth S] FB [auth G], JB [auth I], MB [auth M], PB [auth O], UB [auth S], VA [auth A], XB [auth U], ZA [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain FB [auth G] Focus chain JB [auth I] Focus chain MB [auth M] Focus chain PB [auth O] Focus chain UB [auth S] Focus chain VA [auth A] Focus chain XB [auth U] Focus chain ZA [auth C] Interactions & Density Focus chain FB [auth G] Focus chain JB [auth I] Focus chain MB [auth M] Focus chain PB [auth O] Focus chain UB [auth S] Focus chain VA [auth A] Focus chain XB [auth U] Focus chain ZA [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain HB [auth H] SDF format, chain RB [auth P] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain RB [auth P] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain RB [auth P]	BB [auth D], CB [auth D], HB [auth H], RB [auth P]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BB [auth D] Focus chain CB [auth D] Focus chain HB [auth H] Focus chain RB [auth P] Interactions & Density Focus chain BB [auth D] Focus chain CB [auth D] Focus chain HB [auth H] Focus chain RB [auth P]
OXL Query on OXL Download:Ideal Coordinates CCD File SDF format, chain SB [auth P] MOL2 format, chain SB [auth P] mmCIF format, chain SB [auth P]	SB [auth P]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain SB [auth P] Interactions & Density Focus chain SB [auth P]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain XA [auth B] MOL2 format, chain XA [auth B] mmCIF format, chain XA [auth B]	XA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain XA [auth B] Interactions & Density Focus chain XA [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain DB [auth D] MOL2 format, chain DB [auth D] mmCIF format, chain DB [auth D]	DB [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DB [auth D] Interactions & Density Focus chain DB [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain GB [auth H] SDF format, chain KB [auth J] SDF format, chain NB [auth N] SDF format, chain QB [auth P] SDF format, chain VB [auth T] SDF format, chain WA [auth B] SDF format, chain YB [auth V] MOL2 format, chain AB [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain KB [auth J] MOL2 format, chain NB [auth N] MOL2 format, chain QB [auth P] MOL2 format, chain VB [auth T] MOL2 format, chain WA [auth B] MOL2 format, chain YB [auth V] mmCIF format, chain AB [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain KB [auth J] mmCIF format, chain NB [auth N] mmCIF format, chain QB [auth P] mmCIF format, chain VB [auth T] mmCIF format, chain WA [auth B] mmCIF format, chain YB [auth V]	AB [auth D] GB [auth H] KB [auth J] NB [auth N] QB [auth P] AB [auth D], GB [auth H], KB [auth J], NB [auth N], QB [auth P], VB [auth T], WA [auth B], YB [auth V]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain GB [auth H] Focus chain KB [auth J] Focus chain NB [auth N] Focus chain QB [auth P] Focus chain VB [auth T] Focus chain WA [auth B] Focus chain YB [auth V] Interactions & Density Focus chain AB [auth D] Focus chain GB [auth H] Focus chain KB [auth J] Focus chain NB [auth N] Focus chain QB [auth P] Focus chain VB [auth T] Focus chain WA [auth B] Focus chain YB [auth V]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EB [auth G] SDF format, chain IB [auth I] SDF format, chain LB [auth M] SDF format, chain OB [auth O] SDF format, chain TB [auth S] SDF format, chain UA [auth A] SDF format, chain WB [auth U] SDF format, chain YA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain IB [auth I] MOL2 format, chain LB [auth M] MOL2 format, chain OB [auth O] MOL2 format, chain TB [auth S] MOL2 format, chain UA [auth A] MOL2 format, chain WB [auth U] MOL2 format, chain YA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain IB [auth I] mmCIF format, chain LB [auth M] mmCIF format, chain OB [auth O] mmCIF format, chain TB [auth S] mmCIF format, chain UA [auth A] mmCIF format, chain WB [auth U] mmCIF format, chain YA [auth C]	EB [auth G] IB [auth I] LB [auth M] OB [auth O] TB [auth S] EB [auth G], IB [auth I], LB [auth M], OB [auth O], TB [auth S], UA [auth A], WB [auth U], YA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EB [auth G] Focus chain IB [auth I] Focus chain LB [auth M] Focus chain OB [auth O] Focus chain TB [auth S] Focus chain UA [auth A] Focus chain WB [auth U] Focus chain YA [auth C] Interactions & Density Focus chain EB [auth G] Focus chain IB [auth I] Focus chain LB [auth M] Focus chain OB [auth O] Focus chain TB [auth S] Focus chain UA [auth A] Focus chain WB [auth U] Focus chain YA [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B, D, H, J, N B, D, H, J, N, P, T, V	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.229 (Depositor), 0.228 (DCC)
R-Value Work: 0.174 (Depositor), 0.175 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 257.022	α = 90
b = 157.196	β = 90
c = 166.56	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
MoRDa	phasing
Coot	model building
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-26

Deposition Author(s):

Pfanzagl, V.

Brito, J.A.

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	33997

Revision History (Full details and data files)

Version 1.0: 2022-10-26
Type: Initial release
Version 1.1: 2022-11-09
Changes: Database references
Version 2.0: 2022-12-07
Changes: Advisory, Atomic model
Version 2.1: 2024-01-31
Changes: Data collection, Refinement description
Version 3.0: 2025-10-01
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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7Z53 | pdb_00007z53

Structure of native leukocyte myeloperoxidase in complex with a truncated version (SPIN truncated) of the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus

Literature

The staphylococcal inhibitory protein SPIN binds to human myeloperoxidase with picomolar affinity but only dampens halide oxidation.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)