5MFA | pdb_00005mfa

Crystal structure of human promyeloperoxidase (proMPO)

• PDB DOI: https://doi.org/10.2210/pdb5MFA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2016-11-17 Released: 2017-04-05 
• Deposition Author(s): Grishkovskaya, I., Furtmueller, P.G., Obinger, C., Djinovic-Carugo, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.143 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Starting Model: experimental

Literature

Structure of human promyeloperoxidase (proMPO) and the role of the propeptide in processing and maturation.

Grishkovskaya, I., Paumann-Page, M., Tscheliessnig, R., Stampler, J., Hofbauer, S., Soudi, M., Sevcnikar, B., Oostenbrink, C., Furtmuller, P.G., Djinovic-Carugo, K., Nauseef, W.M., Obinger, C.

(2017) J Biological Chem 292: 8244-8261

• PubMed: 28348079 
• DOI: https://doi.org/10.1074/jbc.M117.775031
• Primary Citation Related Structures: 
  5MFA


• PubMed Abstract: 
  

  Myeloperoxidase (MPO) is synthesized by neutrophil and monocyte precursor cells and contributes to host defense by mediating microbial killing. Although several steps in MPO biosynthesis and processing have been elucidated, many questions remained, such as the structure-function relationship of monomeric unprocessed proMPO versus the mature dimeric MPO and the functional role of the propeptide. Here we have presented the first and high resolution (at 1.25 Å) crystal structure of proMPO and its solution structure obtained by small-angle X-ray scattering. Promyeloperoxidase hosts five occupied glycosylation sites and six intrachain cystine bridges with Cys-158 of the very flexible N-terminal propeptide being covalently linked to Cys-319 and thereby hindering homodimerization. Furthermore, the structure revealed (i) the binding site of proMPO-processing proconvertase, (ii) the structural motif for subsequent cleavage to the heavy and light chains of mature MPO protomers, and (iii) three covalent bonds between heme and the protein. Studies of the mutants C158A, C319A, and C158A/C319A demonstrated significant differences from the wild-type protein, including diminished enzymatic activity and prevention of export to the Golgi due to prolonged association with the chaperone calnexin. These structural and functional findings provide novel insights into MPO biosynthesis and processing.

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Organizational Affiliation: 
• Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria.
Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, A-1190 Vienna, Austria.
Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, A-1190 Vienna, Austria.
Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Veĉna pot 113, 1000 Ljubljana, Slovenia.
Inflammation Program and Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242. Electronic address: [e-mail].
Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.74 kDa 
• Atom Count: 5,972 
• Modeled Residue Count: 588 
• Deposited Residue Count: 697 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloperoxidase	A	697	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 GTEx:  ENSG00000005381
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P05164-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	D	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	G [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	S [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.20 Å
• R-Value Free:  0.143 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.152	α = 90
b = 109.151	β = 122.66
c = 83.961	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Grishkovskaya, I., Furtmueller, P.G., Obinger, C., Djinovic-Carugo, K.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary