4XJK

Crystal structure of Mn(II) Ca(II) Na(I) bound calprotectin

  • Classification: METAL BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2015-01-08 Released: 2015-04-15 
  • Deposition Author(s): Drennan, C.L., Bowman, S.E.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), National Science Foundation (NSF, United States), National Institutes of Health/Office of the Director, Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Manganese Binding Properties of Human Calprotectin under Conditions of High and Low Calcium: X-ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis.

Gagnon, D.M.Brophy, M.B.Bowman, S.E.Stich, T.A.Drennan, C.L.Britt, R.D.Nolan, E.M.

(2015) J Am Chem Soc 137: 3004-3016

  • DOI: 10.1021/ja512204s
  • Primary Citation of Related Structures:  
    4XJK

  • PubMed Abstract: 
  • The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation ...

    The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Herein, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimer is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin-echo envelope modulation and electron-nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed (15)N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by two to three orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin.


    Organizational Affiliation

    Department of Chemistry, University of California , Davis, California 95616, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A8 ACEGI93Homo sapiensMutation(s): 1 
Gene Names: S100A8CAGACFAGMRP8
Find proteins for P05109 (Homo sapiens)
Explore P05109 
Go to UniProtKB:  P05109
NIH Common Fund Data Resources
PHAROS:  P05109
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A9 BDFHJ114Homo sapiensMutation(s): 1 
Gene Names: S100A9CAGBCFAGMRP14
Find proteins for P06702 (Homo sapiens)
Explore P06702 
Go to UniProtKB:  P06702
NIH Common Fund Data Resources
PHAROS:  P06702
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
A, C, E, G, I
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.279α = 90
b = 49.239β = 94.07
c = 218.067γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069857
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099257
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403
Department of Energy (DOE, United States)United StatesDE-AC02-06-CH11357
National Science Foundation (NSF, United States)United States1352132
National Institutes of Health/Office of the DirectorUnited States1DP2OD007045-01
Department of Energy (DOE, United States)United StatesDE-FG02-11ER16282
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence