1HLB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 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


  • 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 ...

    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
    • 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
    • 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
    • N-Terminal Substitution of Some Sea Cucumber Hemoglobins
      Kitto, G.B.,Erwin, D.,West, R.,Omnaas, J.
      (1976) COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. 55: 105


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (DEOXY)
A
158Caudina arenicolaN/A
Find proteins for P80018 (Caudina arenicola)
Go to UniProtKB:  P80018
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.740α = 90.00
b = 45.230β = 104.40
c = 40.920γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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