1LLA

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

PDB DOI: 10.2210/pdb1LLA/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Limulus polyphemus
Mutation(s): No

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

Experimental Data Snapshot

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

PubMed: 8518732 Search on PubMedSearch on PubMed Central
DOI: 10.1002/pro.5560020411
Primary Citation of Related Structures:
1LLA, 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 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:

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

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOCYANIN (SUBUNIT TYPE II)	A	628	Limulus polyphemus	Mutation(s): 0
UniProt
Find proteins for P04253 (Limulus polyphemus) Explore P04253 Go to UniProtKB: P04253
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04253
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction