3ZHW: X-ray Crystallographic Structural Characteristics Of Arabidopsis Hemoglobin I And Their Functional Implications

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 2.2A 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.
PDB ID: 3ZHWDownload
MMDB ID: 108073
PDB Deposition Date: 2012/12/30
Updated in MMDB: 2013/08
Experimental Method:
x-ray diffraction
Resolution: 2.22  Å
Source Organism:
Similar Structures:
Biological Unit for 3ZHW: monomeric; determined by author and by software (PISA)
Molecular Components in 3ZHW
Label Count Molecule
Protein (1 molecule)
Non-symbiotic Hemoglobin 1(Gene symbol: HB1)
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB