8W3A

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D

This is a non-PDB format compatible entry.

Summary for 8W3A

• Entry DOI: 10.2210/pdb8w3a/pdb
• Related: 8VSH
• Descriptor: Group 1 truncated hemoglobin, PROTOPORPHYRIN IX CONTAINING FE, {3-[(2R,5'R)-9',14'-diethenyl-5'-hydroxy-5',10',15',19'-tetramethyl-5-oxo-4,5-dihydro-3H-spiro[furan-2,4'-[21,22,23,24]tetraazapentacyclo[16.2.1.13,6.18,11.113,16]tetracosa[1,3(24),6,8,10,12,14,16(22),17,19]decaen]-20'-yl-kappa~4~N~21'~,N~22'~,N~23'~,N~24'~]propanoato}iron, ... (4 entities in total)
• Functional Keywords: globin, 2/2 hemoglobin, heme binding protein, psychropiezophile, heme-binding protein
• Biological source: Shewanella benthica KT99
• Total number of polymer chains: 4
• Total formula weight: 56349.60

Authors

Lecomte, J.T.J.,Schlessman, J.L.,Schultz, T.D.,Siegler, M.A. (deposition date: 2024-02-22, release date: 2024-04-03, Last modification date: 2024-07-17)

Primary citation

Martinez Grundman, J.E.,Schultz, T.D.,Schlessman, J.L.,Liu, K.,Johnson, E.A.,Lecomte, J.T.J.
Heme d formation in a Shewanella benthica hemoglobin.
J.Inorg.Biochem., 259:112654-112654, 2024

PubMed Abstract: In our continued investigations of microbial globins, we solved the structure of a truncated hemoglobin from Shewanella benthica, an obligate psychropiezophilic bacterium. The distal side of the heme active site is lined mostly with hydrophobic residues, with the exception of a tyrosine, Tyr34 (CD1) and a histidine, His24 (B13). We found that purified SbHbN, when crystallized in the ferric form with polyethylene glycol as precipitant, turned into a green color over weeks. The electron density obtained from the green crystals accommodated a trans heme d, a chlorin-type derivative featuring a γ-spirolactone and a vicinal hydroxyl group on a pyrroline ring. In solution, exposure of the protein to one equivalent of hydrogen peroxide resulted in a similar green color change, but caused by the formation of multiple products. These were oxidation species released on protein denaturation, likely including heme d, and a species with heme covalently attached to the polypeptide. The Tyr34Phe replacement prevented the formation of both heme d and the covalent linkage. The ready modification of heme b by SbHbN expands the range of chemistries supported by the globin fold and offers a route to a novel heme cofactor.

PubMed: 38959524
DOI: 10.1016/j.jinorgbio.2024.112654

Experimental method

X-RAY DIFFRACTION (1.8 Å)