1LLA

CRYSTAL STRUCTURE OF DEOXYGENATED LIMULUS POLYPHEMUS SUBUNIT II HEMOCYANIN AT 2.18 ANGSTROMS RESOLUTION: CLUES FOR A MECHANISM FOR ALLOSTERIC REGULATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of deoxygenated Limulus polyphemus subunit II hemocyanin at 2.18 A resolution: clues for a mechanism for allosteric regulation.

Hazes, B.Magnus, K.A.Bonaventura, C.Bonaventura, J.Dauter, Z.Kalk, K.H.Hol, W.G.

(1993) Protein Sci. 2: 597-619

  • DOI: 10.1002/pro.5560020411
  • Primary Citation of Related Structures:  1NOL

  • PubMed Abstract: 
  • The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 A. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacem ...

    The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 A. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacement using the crustacean hemocyanin structure of Panulirus interruptus. The most striking observation in the Limulus structure is the unexpectedly large distance of 4.6 A between both copper ions in the oxygen-binding site. Each copper has approximate trigonal planar coordination by three histidine N epsilon atoms. No bridging ligand between the copper ions could be detected. Other important new discoveries are (1) the presence of a cis-peptide bond between Glu 309 and Ser 310, with the carbonyl oxygen of the peptide plane hydrogen bonded to the N delta atom of the copper B ligand His 324; (2) localization of a chloride-binding site in the interface between the first and second domain; (3) localization of a putative calcium-binding site in the third domain. Furthermore, comparison of Limulus versus Panulirus hemocyanin revealed considerable tertiary and quaternary rigid body movements, although the overall folds are similar. Within the subunit, the first domain is rotated by about 7.5 degrees with respect to the other two domains, whereas within the hexamer the major movement is a 3.1 degrees rotation of the trimers with respect to each other. The rigid body rotation of the first domain suggests a structural mechanism for the allosteric regulation by chloride ions and probably causes the cooperative transition of the hexamer between low and high oxygen affinity states. In this postulated mechanism, the fully conserved Phe49 is the key residue that couples conformational changes of the dinuclear copper site into movements of the first domain.


    Related Citations: 
    • Crystal Structure of Hexameric Haemocyanin from Panulirus Interruptus Refined at 3.2 Angstroms Resolution
      Volbeda, A.,Hol, W.G.J.
      (1989) J.Mol.Biol. 209: 249
    • Structure of Hemocyanin II from the Horshoe Crab Limulus Polyphemus
      Nakashima, H.,Behrens, P.Q.,Moore, M.D.,Yokota, E.,Riggs, A.F.
      (1986) J.Biol.Chem. 261: 10526
    • Hexamers of Subunit II from Limulus Hemocyanin (A 48-mer) Have the Same Quaternary Structure as Whole Panulirus Hemocyanin Molecules
      Magnus, K.A.,Lattman, E.E.,Volbeda, A.,Hol, W.G.J.
      (1991) Proteins 9: 240


    Organizational Affiliation

    BIOSON Research Institute, Department of Chemistry, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOCYANIN (SUBUNIT TYPE II)
A
628Limulus polyphemusN/A
Find proteins for P04253 (Limulus polyphemus)
Go to UniProtKB:  P04253
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Work: 0.174 
  • Space Group: R 3 2
Unit Cell:
Length (Å)Angle (°)
a = 117.002α = 60.02
b = 117.002β = 60.02
c = 117.002γ = 60.02
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1992-09-07 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Hazes, B., Hol, W.G.J.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance