Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 73.85 kDa 
• Atom Count: 5,432 
• Modelled Residue Count: 634 
• Deposited Residue Count: 637 
• Unique protein chains: 2

 6AZP

A Structurally Dynamic N-terminal Region Drives Function of the Staphylococcal Peroxidase Inhibitor (SPIN)

• PDB DOI: 10.2210/pdb6AZP/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens, Staphylococcus aureus
• Expression System: Mus musculus, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-11 Released: 2017-12-27 
• Deposition Author(s): Ramyar, K.X., Geisbrecht, B.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.229 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Literature

A structurally dynamic N-terminal region drives function of the staphylococcal peroxidase inhibitor (SPIN).

de Jong, N.W.M., Ploscariu, N.T., Ramyar, K.X., Garcia, B.L., Herrera, A.I., Prakash, O., Katz, B.B., Leidal, K.G., Nauseef, W.M., van Kessel, K.P.M., van Strijp, J.A.G., Geisbrecht, B.V.

(2018) J Biol Chem 293: 2260-2271

• PubMed: 29306874 
• DOI: 10.1074/jbc.RA117.000134
• Primary Citation of Related Structures:  
  6AZP


• PubMed Abstract: 
  

The heme-containing enzyme myeloperoxidase (MPO) is critical for optimal antimicrobial activity of human neutrophils. We recently discovered that the bacterium Staphylococcus aureus expresses a novel immune evasion protein, called SPIN, that binds tightly to MPO, inhibits MPO activity, and contributes to bacterial survival following phagocytosis. A co-crystal structure of SPIN bound to MPO suggested that SPIN blocks substrate access to the catalytic heme by inserting an N-terminal β-hairpin into the MPO active-site channel. Here, we describe a series of experiments that more completely define the structure/function relationships of SPIN. Whereas the SPIN N terminus adopts a β-hairpin confirmation upon binding to MPO, the solution NMR studies presented here are consistent with this region of SPIN being dynamically structured in the unbound state. Curiously, whereas the N-terminal β-hairpin of SPIN accounts for ∼55% of the buried surface area in the SPIN-MPO complex, its deletion did not significantly change the affinity of SPIN for MPO but did eliminate the ability of SPIN to inhibit MPO. The flexible nature of the SPIN N terminus rendered it susceptible to proteolytic degradation by a series of chymotrypsin-like proteases found within neutrophil granules, thereby abrogating SPIN activity. Degradation of SPIN was prevented by the S. aureus immune evasion protein Eap, which acts as a selective inhibitor of neutrophil serine proteases. Together, these studies provide insight into MPO inhibition by SPIN and suggest possible functional synergy between two distinct classes of S. aureus immune evasion proteins.

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Organizational Affiliation: 

the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase	A	577	Homo sapiens	Mutation(s): 0  Gene Names: MPO 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal Peroxidase Inhibitor	B	60	Staphylococcus aureus	Mutation(s): 0  Gene Names: SAMEA3448974_01858
UniProt
Find proteins for Q2G0X2 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0X2  Go to UniProtKB:  Q2G0X2

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	E [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.229 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.854	α = 90
b = 92.876	β = 119.91
c = 80.46	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Ramyar, K.X., Geisbrecht, B.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM121511
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI111203

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 1.2: 2018-02-28
  Changes: Database references
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary