1CXP

CRYOGENIC CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE ISOFORM C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report



Literature

X-ray crystal structure and characterization of halide-binding sites of human myeloperoxidase at 1.8 A resolution.

Fiedler, T.J.Davey, C.A.Fenna, R.E.

(2000) J Biol Chem 275: 11964-11971

  • DOI: 10.1074/jbc.275.16.11964
  • Primary Citation of Related Structures:  
    1D2V, 1CXP

  • PubMed Abstract: 
  • The x-ray crystal structure of human myeloperoxidase has been extended to 1.8 A resolution, using x-ray data recorded at -180 degrees C (r = 0.197, free r = 0.239). Results confirm that the heme is covalently attached to the protein via two ester lin ...

    The x-ray crystal structure of human myeloperoxidase has been extended to 1.8 A resolution, using x-ray data recorded at -180 degrees C (r = 0.197, free r = 0.239). Results confirm that the heme is covalently attached to the protein via two ester linkages between the carboxyl groups of Glu(242) and Asp(94) and modified methyl groups on pyrrole rings A and C of the heme as well as a sulfonium ion linkage between the sulfur atom of Met(243) and the beta-carbon of the vinyl group on pyrrole ring A. In the native enzyme a bound chloride ion has been identified at the amino terminus of the helix containing the proximal His(336). Determination of the x-ray crystal structure of a myeloperoxidase-bromide complex (r = 0.243, free r = 0.296) has shown that this chloride ion can be replaced by bromide. Bromide is also seen to bind, at partial occupancy, in the distal heme cavity, in close proximity to the distal His(95), where it replaces the water molecule hydrogen bonded to Gln(91). The bromide-binding site in the distal cavity appears to be the halide-binding site responsible for shifts in the Soret band of the absorption spectrum of myeloperoxidase. It is proposed that halide binding to this site inhibits the enzyme by effectively competing with H(2)O(2) for access to the distal histidine, whereas in compound I, the same site may be the halide substrate-binding site.


    Related Citations: 
    • Structure of the Green Heme in Myeloperoxidase
      Fenna, R., Zeng, J., Davey, C.
      (1995) Arch Biochem Biophys 316: 653
    • 2.3 Angstrom Resolution X-Ray Crystal Structure of the Bisubstrate Analogue Inhibitor Salicylhydroxamic Acid Bound to Human Myeloperoxidase: A Model for a Prereaction Complex with Hydrogen Peroxide
      Davey, C.A., Fenna, R.E.
      (1996) Biochemistry 35: 10967
    • X-Ray Crystal Structure of Canine Myeloperoxidase at 3 Angstrom Resolution
      Zeng, J., Fenna, R.E.
      (1992) J Mol Biol 226: 185
    • Site-Directed Mutagenesis of Human Myeloperoxidase: Further Identification of Residues Involved in Catalytic Activity and Heme Interaction
      Jacquet, A., Garcia-Quintana, L., Deleersnyder, V., Fenna, R., Bollen, A., Moguilevsky, N.
      (1994) Biochem Biophys Res Commun 202: 73

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Miami Medical School, Miami, Florida 33136, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MYELOPEROXIDASEAB104Homo sapiensMutation(s): 0 
Gene Names: MPO
EC: 1.11.1.7 (PDB Primary Data), 1.11.2.2 (UniProt)
Find proteins for P05164 (Homo sapiens)
Explore P05164 
Go to UniProtKB:  P05164
NIH Common Fund Data Resources
PHAROS  P05164
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MYELOPEROXIDASECD466Homo sapiensMutation(s): 1 
Gene Names: MPO
EC: 1.11.1.7 (PDB Primary Data), 1.11.2.2 (UniProt)
Find proteins for P05164 (Homo sapiens)
Explore P05164 
Go to UniProtKB:  P05164
NIH Common Fund Data Resources
PHAROS  P05164
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D 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
E, F
6 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download CCD File 
C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
C,DL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.03α = 90
b = 63.38β = 97.36
c = 92.17γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary