3DR9

Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase from Amphitrite ornata

Summary for 3DR9

• Entry DOI: 10.2210/pdb3dr9/pdb
• Descriptor: Dehaloperoxidase A, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: deoxy form of dehaloperoxidase, dhp, heme peroxidase, globin-like, globin, heme protein, heme, oxygen transport, peroxidase, transport, oxidoreductase
• Biological source: Amphitrite ornata
• Total number of polymer chains: 2
• Total formula weight: 32618.36

Authors

Chen, X.,de Serrano, V.S.,Betts, L.,Franzen, S. (deposition date: 2008-07-10, release date: 2009-01-27, Last modification date: 2024-02-21)

Primary citation

Chen, Z.,de Serrano, V.,Betts, L.,Franzen, S.
Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata.
Acta Crystallogr.,Sect.D, 65:34-40, 2009

PubMed Abstract: The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein which has a globin fold but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. As a hemoglobin, DHP cycles between the oxy and deoxy states as it reversibly binds oxygen for storage. Here, it is reported that the distal histidine, His55, exhibits conformational flexibility in the deoxy form and is consequently observed in two solvent-exposed conformations more than 9.5 A away from the heme. These conformations are analogous to the open conformation of sperm whale myoglobin. The heme iron in deoxy ferrous DHP is five-coordinate and has an out-of-plane displacement of 0.25 A from the heme plane. The observation of five-coordinate heme iron with His55 in a remote solvent-exposed conformation is consistent with the hypothesis that His55 interacts with heme iron ligands through hydrogen bonding in the closed conformation. Since His55 is also displaced by the binding of 4-iodophenol in an internal pocket, these results provide new insight into the correlation between heme iron ligation, molecular binding in the distal pocket and the conformation of the distal histidine in DHP.

PubMed: 19153464
DOI: 10.1107/S0907444908036548

Experimental method

X-RAY DIFFRACTION (1.26 Å)