1OXY

CRYSTALLOGRAPHIC ANALYSIS OF OXYGENATED AND DEOXYGENATED STATES OF ARTHROPOD HEMOCYANIN SHOWS UNUSUAL DIFFERENCES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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This is version 1.2 of the entry. See complete history


Literature

Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences.

Magnus, K.A.Hazes, B.Ton-That, H.Bonaventura, C.Bonaventura, J.Hol, W.G.

(1994) Proteins 19: 302-309

  • DOI: 10.1002/prot.340190405
  • Primary Citation of Related Structures:  
    1OXY

  • PubMed Abstract: 
  • The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 A resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the space ...

    The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 A resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the space group R32 with one subunit per asymmetric unit forming hexamers with 32 point group symmetry. Molecular oxygen is bound to a dinuclear copper center in the protein's second domain, symmetrically between and equidistant from the two copper atoms. The copper-copper distance in oxygenated Limulus hemocyanin is 3.6 +/- 0.2 A, which is surprisingly 1 A less than that seen previously in deoxygenated Limulus polyphemus subunit II hemocyanin (Hazes et al., Protein Sci. 2:597, 1993). Away from the oxygen binding sites, the tertiary and quaternary structures of oxygenated and deoxygenated Limulus subunit II hemocyanins are quite similar. A major difference in tertiary structures is seen, however, when the Limulus structures are compared with deoxygenated Panulirus interruptus hemocyanin (Volbeda, A., Hol, W.G.J.J. Mol. Biol. 209:249, 1989) where the position of domain 1 is rotated by 8 degrees with respect to domains 2 and 3. We postulate this rotation plays an important role in cooperativity and regulation of oxygen affinity in all arthropod hemocyanins.


    Related Citations: 
    • Hexamers of Subunit II from Limulus Hemocyanin (A 48mer) Have the Same Quaternary Structure as Whole Panulirus Hemocyanin Molecules
      Magnus, K.A., Lattman, E.E., Volbeda, A., Hol, W.G.L.
      (1991) Proteins 9: 240
    • Crystals of a Functional 70,000 Molecular Weight Subunit of Hemocyanin from Limulus Polyphemus
      Magnus, K.A., Love, W.E.
      (1977) J Mol Biol 116: 171

    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106-4935.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMOCYANIN (SUBUNIT TYPE II) A628Limulus polyphemusMutation(s): 0 
Find proteins for P04253 (Limulus polyphemus)
Explore P04253 
Go to UniProtKB:  P04253
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
OXY
Query on OXY

Download Ideal Coordinates CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.24α = 90
b = 117.24β = 90
c = 285.86γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance