5GJ3

Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in two-heme bound form (holo-2)

Summary for 5GJ3

• Entry DOI: 10.2210/pdb5gj3/pdb
• Related: 5GIZ 5GJ0 5GJ1 5GJ2
• Descriptor: Periplasmic binding protein, PROTOPORPHYRIN IX CONTAINING FE, ZINC ION, ... (4 entities in total)
• Functional Keywords: metal transport, transport protein
• Biological source: Roseiflexus sp. RS-1
• Total number of polymer chains: 1
• Total formula weight: 29740.93

Authors

Rahman, M.M.,Naoe, Y.,Nakamura, N.,Shiro, Y.,Sugimoto, H. (deposition date: 2016-06-26, release date: 2017-06-28, Last modification date: 2023-11-08)

Primary citation

Naoe, Y.,Nakamura, N.,Rahman, M.M.,Tosha, T.,Nagatoishi, S.,Tsumoto, K.,Shiro, Y.,Sugimoto, H.
Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Proteins, 85:2217-2230, 2017

PubMed Abstract: Periplasmic heme-binding proteins (PBPs) in Gram-negative bacteria are components of the heme acquisition system. These proteins shuttle heme across the periplasmic space from outer membrane receptors to ATP-binding cassette (ABC) heme importers located in the inner-membrane. In the present study, we characterized the structures of PBPs found in the pathogen Burkholderia cenocepacia (BhuT) and in the thermophile Roseiflexus sp. RS-1 (RhuT) in the heme-free and heme-bound forms. The conserved motif, in which a well-conserved Tyr interacts with the nearby Arg coordinates on heme iron, was observed in both PBPs. The heme was recognized by its surroundings in a variety of manners including hydrophobic interactions and hydrogen bonds, which was confirmed by isothermal titration calorimetry. Furthermore, this study of 3 forms of BhuT allowed the first structural comparison and showed that the heme-binding cleft of BhuT adopts an "open" state in the heme-free and 2-heme-bound forms, and a "closed" state in the one-heme-bound form with unique conformational changes. Such a conformational change might adjust the interaction of the heme(s) with the residues in PBP and facilitate the transfer of the heme into the translocation channel of the importer.

PubMed: 28913898
DOI: 10.1002/prot.25386

Experimental method

X-RAY DIFFRACTION (2 Å)