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 
  • R-Value Observed: 0.133 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1093/emboj/19.11.2424
  • Primary Citation of Related Structures:  
    1DLW, 1DLY

  • 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). 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMOGLOBIN116Paramecium caudatumMutation(s): 0 
UniProt
Find proteins for P15160 (Paramecium caudatum)
Explore P15160 
Go to UniProtKB:  P15160
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15160
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.18α = 90
b = 61.18β = 90
c = 35.79γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
WARPmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations