4NK1 image
Deposition Date 2013-11-12
Release Date 2014-09-24
Last Version Date 2023-09-20
Entry Detail
PDB ID:
4NK1
Keywords:
Title:
Crystal structure of phosphate-bound Hell's gate globin IV
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.21 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Hemoglobin-like protein
Gene (Uniprot):Minf_1222
Chain IDs:A, B
Chain Length:193
Number of Molecules:2
Biological Source:Methylacidiphilum infernorum
Primary Citation
Crystal structure of truncated haemoglobin from an extremely thermophilic and acidophilic bacterium.
J.Biochem. 156 97 106 (2014)
PMID: 24733432 DOI: 10.1093/jb/mvu023

Abstact

A truncated haemoglobin (tHb) has been identified in an acidophilic and thermophilic methanotroph Methylacidiphilium infernorum. Hell's Gate Globin IV (HGbIV) and its related tHbs differ from all other bacterial tHbs due to their distinctively large sequence and polar distal haem pocket residues. Here we report the crystal structure of HGbIV determined at 1.96 Å resolution. The HGbIV structure has the distinctive 2/2 α-helical structure with extensions at both termini. It has a large distal site cavity in the haem pocket surrounded by four polar residues: His70(B9), His71(B10), Ser97(E11) and Trp137(G8). This cavity can bind bulky ligands such as a phosphate ion. Conformational shifts of His71(B10), Leu90(E4) and Leu93(E7) can also provide more space to accommodate larger ligands than the phosphate ion. The entrance/exit of such bulky ligands might be facilitated by positional flexibility in the CD1 loop, E helix and haem-propionate A. Therefore, the large cavity in HGbIV with polar His70(B9) and His71(B10), in contrast to the distal sites of other bacterial tHbs surrounded by non-polar residues, suggests its distinct physiological functions.

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