1HLB

Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola.

Mitchell, D.T.Kitto, G.B.Hackert, M.L.

(1995) J Mol Biol 251: 421-431

  • DOI: 10.1006/jmbi.1995.0445
  • Primary Citation of Related Structures:  
    1HLB

  • PubMed Abstract: 
  • The X-ray structures of two hemoglobins (Hb) from the sea cucumber Caudina arenicola (an echinoderm) have been determined: a low spin, hemichrome, monomeric Hb-C chain, and a cyanomet-liganded dimeric Hb-D chain. Attempts to obtain crystal structures of the deoxy-liganded and hemichrome forms from the same chain type have not been successful ...

    The X-ray structures of two hemoglobins (Hb) from the sea cucumber Caudina arenicola (an echinoderm) have been determined: a low spin, hemichrome, monomeric Hb-C chain, and a cyanomet-liganded dimeric Hb-D chain. Attempts to obtain crystal structures of the deoxy-liganded and hemichrome forms from the same chain type have not been successful. In this work, the Hb-C chain and Hb-D chain structures are compared, and differences observed in tertiary structure related to the different ligand states for hemoglobin chains from this organism. In addition to shifts of the distal histidine and E helix, differences are noted in the position of the heme group within the heme pocket, the hydrogen bonding of the heme group to the protein, and the status of the D helix. These differences are important in understanding the ligand-linked association states of these hemoglobins. The quaternary structure of the Hb-D homodimer is compared with those from two other invertebrate hemoglobins from Scapharca inaequivalvis and Urechis caupo, which also have subunit-subunit interactions that involve the E and E' helices. The dimer interactions of the Caudina and Urechis hemoglobins are quite dissimilar. However, the dimer interface observed in cyanomet Hb-D is strikingly similar to that observed for the carbonmonoxy hemoglobin dimer from the clam, Scapharca, yet many of the key amino acid residues implicated in the cooperative mechanism of the Scapharca hemoglobin are not conserved in the Caudina hemoglobins.


    Related Citations: 
    • Amino Acid Sequence of the Coelomic C Globin from the Sea Cucumber Caudina (Molpadia) Arenicola
      Mcdonald, G.D., Davidson, L., Kitto, G.B.
      (1992) J Protein Chem 11: 29
    • Preliminary Crystallographic Data on Monomeric and Dimeric Hemoglobins from the Sea Cucumber, Molpadia Arenicola
      Carson, W.M., Bowers, T.R., Kitto, G.B., Hackert, M.L.
      (1979) J Biol Chem 254: 7400
    • Functional Consequences of Ligand-Linked Dissociation in Hemoglobin from the Sea Cucumber Molpadia Arenicola
      Bonaventura, C., Bonaventura, J., Kitto, B., Brunori, M., Antonini, E.
      (1976) Biochim Biophys Acta 428: 779
    • N-Terminal Substitution of Some Sea Cucumber Hemoglobins
      Kitto, G.B., Erwin, D., West, R., Omnaas, J.
      (1976) Comp Biochem Physiol B 55: 105

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas at Austin 78712, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMOGLOBIN (DEOXY) A158Molpadia arenicolaMutation(s): 0 
Find proteins for P80018 (Molpadia arenicola)
Explore P80018 
Go to UniProtKB:  P80018
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.74α = 90
b = 45.23β = 104.4
c = 40.92γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other