3ZHW

X-ray Crystallographic Structural Characteristics of Arabidopsis Hemoglobin I and their Functional Implications


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-Ray Crystallographic Structural Characteristics of Arabidopsis Hemoglobin I and Their Functional Implications

Mukhi, N.Dhindwal, S.Uppal, S.Kumar, P.Kaur, J.Kundu, S.

(2013) Biochim.Biophys.Acta 1834: 1944

  • DOI: 10.1016/j.bbapap.2013.02.024

  • PubMed Abstract: 
  • Genome of the model dicot flowering plant, Arabidopsis thaliana, a popular tool for understanding molecular biology of plant physiology, encodes all three classes of plant hemoglobins that differ in their sequence, ligand binding and spectral propert ...

    Genome of the model dicot flowering plant, Arabidopsis thaliana, a popular tool for understanding molecular biology of plant physiology, encodes all three classes of plant hemoglobins that differ in their sequence, ligand binding and spectral properties. As such these globins are of considerable attention. Crystal structures of few members of plant class I nonsymbiotic hemoglobin have been described earlier. Here we report the crystal structure of Arabidopsis class I hemoglobin (AHb1) to 2.2วบ and compare its key features with the structures of similar nonsymbiotic hemoglobin from other species. Crystal structure of AHb1 is homologous to the related members with similar globin fold and heme pocket architecture. The structure is homodimeric in the asymmetric unit with both distal and proximal histidines coordinating to the heme iron atom. Residues lining the dimeric interface are also conserved in AHb1 with the exception of additional electrostatic interaction between H112 and E113 of each subunit and that involving Y119 through two water molecules. In addition, differences in heme pocket non-covalent interactions, a novel Ser residue at F7 position, Xe binding site variability, internal cavity topology differences, CD loop conformation and stability and other such properties might explain kinetic variability in AHb1. Detailed cavity analysis of AHb1 showed the presence of a novel long tunnel connecting the distal pockets of both the monomers. Presence of such tunnel, along with conformational heterogeneity observed in the two chains, might suggest cooperative ligand binding and support its role in NO scavenging. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.


    Organizational Affiliation

    Department of Genetics, University of Delhi South Campus, New Delhi, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NON-SYMBIOTIC HEMOGLOBIN 1
A, B
160Arabidopsis thalianaMutation(s): 0 
Gene Names: AHB1 (GLB1)
Find proteins for O24520 (Arabidopsis thaliana)
Go to UniProtKB:  O24520
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
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: 2.22 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.280α = 90.00
b = 76.672β = 90.00
c = 98.228γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references
  • Version 1.2: 2013-08-07
    Type: Database references
  • Version 1.3: 2014-02-12
    Type: Source and taxonomy