4NK2

Crystal structure of Hell's gate globin IV

Summary for 4NK2

• Entry DOI: 10.2210/pdb4nk2/pdb
• Descriptor: Hemoglobin-like protein, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: truncated, hemoglobins, heme, truncated hemoglobin, oxygen binding
• Biological source: Methylacidiphilum infernorum
• Total number of polymer chains: 2
• Total formula weight: 46639.64

Authors

Jamil, F. (deposition date: 2013-11-12, release date: 2014-09-24, Last modification date: 2023-09-20)

Primary citation

Jamil, F.,Teh, A.H.,Schadich, E.,Saito, J.A.,Najimudin, N.,Alam, M.
Crystal structure of truncated haemoglobin from an extremely thermophilic and acidophilic bacterium.
J.Biochem., 156:97-106, 2014

PubMed Abstract: 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.

PubMed: 24733432
DOI: 10.1093/jb/mvu023

Experimental method

X-RAY DIFFRACTION (1.96 Å)