1DLW

X-RAY CRYSTAL STRUCTURE OF TRUNCATED HEMOGLOBIN FROM P.CAUDATUM.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.

Pesce, A.Couture, M.Dewilde, S.Guertin, M.Yamauchi, K.Ascenzi, P.Moens, L.Bolognesi, M.

(2000) EMBO J. 19: 2424-2434

  • DOI: 10.1093/emboj/19.11.2424
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small hemoproteins displaying amino acid sequences 20-40 residues shorter than (non-)vertebrate hemoglobins (Hbs) have recently been identified in several pathogenic and non-pathogenic unicellular organisms, and named 'truncated hemoglobins' (trHbs). ...

    Small hemoproteins displaying amino acid sequences 20-40 residues shorter than (non-)vertebrate hemoglobins (Hbs) have recently been identified in several pathogenic and non-pathogenic unicellular organisms, and named 'truncated hemoglobins' (trHbs). They have been proposed to be involved not only in oxygen transport but also in other biological functions, such as protection against reactive nitrogen species, photosynthesis or to act as terminal oxidases. Crystal structures of trHbs from the ciliated protozoan Paramecium caudatum and the green unicellular alga Chlamydomonas eugametos show that the tertiary structure of both proteins is based on a 'two-over-two' alpha-helical sandwich, reflecting an unprecedented editing of the classical 'three-over-three' alpha-helical globin fold. Based on specific Gly-Gly motifs the tertiary structure accommodates the deletion of the N-terminal A-helix and replacement of the crucial heme-binding F-helix with an extended polypeptide loop. Additionally, concerted structural modifications allow burying of the heme group and define the distal site, which hosts a TyrB10, GlnE7 residue pair. A set of structural and amino acid sequence consensus rules for stabilizing the fold and the bound heme in the trHbs homology subfamily is deduced.


    Organizational Affiliation

    Department of Physics - INFM and Advanced Biotechnology Center - IST, University of Genova, Largo Rosanna Benzi 10, 16132 Genova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN
A
116Paramecium caudatumMutation(s): 0 
Find proteins for P15160 (Paramecium caudatum)
Go to UniProtKB:  P15160
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.133 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 61.180α = 90.00
b = 61.180β = 90.00
c = 35.790γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SOLVEphasing
SCALEPACKdata scaling
WARPmodel building
ARP/wARPmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance