Table 2.

Representative available X-ray crystal structures for heme-binding CDE proteins

Family	PDB IDs	Source	Description	Subfamily	Ref.
DyP	2IIZ, 2HAG	Shewanella oneidensis: facultative aerobe, Proteobacterium	Dimeric; Heme-bound and heme-free forms available. Also called prephenate dehydrogenase (TyrA).	Group 2 (Fig. 6)	22,29
	2GVK	Bacteroides thetaiotaomicron: Gram-negative anaerobe; dominant species in human gut	Hexameric; Heme-free structure.	Group 2 (Fig. 6)	29
	3QNS,3QNR, 3VEC, 3VED,3VEE, 3VEF, 3VEG, 4HOV	Rhodococcus jostii: soil-dwelling member of phylum Actinobacterium with robust biodegradative capabilities	Hexameric; homologous to YfeX (E. coli).	Group 2 (Fig. 6)	24, 25
	2D3Q, 3MM1, 3MM2, 3MM3, 3AFV,3VXI,3VXJ	Bjerkandera adusta (formerly Thanatephorus cucumeris): fungus from phylum Basidomycota; causative agent of white rot	Monomeric; structures of mutants and different heme- ligand complexes available.	Group 3 (Fig. 6)	30 31, 76,
	4AU9, 4W7J-O	Auricularia auricula-judae: saprophytic fungus from phylum Basidomycota;	Monomeric	Group 3 (Fig. 6)	26, 40
EfeB	2Y4D,2Y4E, 2Y4F,3O72	Escherichia coli: phyum Proteobacteria	Dimeric; Heme-free, protoporphyrin IX- and heme-bound	Group 1 (Fig. 6)	11, 32
	4GS1	Thermobifida cellulosilytica: lignocellulose-decomposing member of phylum Actinobacterium	Dimeric	Group 1 (Fig. 6)	33
	4GRC, 4GT2, 4GU7	Streptomyces coelicolor: member of phylum Actinobacterium with robust biodegradative capabilities	Dimeric	Group 1 (Fig. 6)	33
Cld	2VXH	Azospira oryzae: Perchlorate respiring member of phylum Proteobacteria	Pentameric in solution, hexameric in solid state	Respiratory Clds (Fig. 7)	4
	3Q08, 3Q09	Dechloromonas aromatica: Perchlorate respiring member of phylum	Pentameric	Respiratory Clds (Fig. 7)	5
	3NN1-4, 4M05-4M09	Candidatus Nitrospira defluvii: non-perchlorate respiring member of phylum Nitrospira. The cld gene is suggested to have been laterally transferred from a respirer.	Pentameric	Respiratory Clds (Fig. 7)	6, 38
	3QPI	Nitrobacter winogradskyii: non-perchlorate respiring member of phylum Proteobacteria.	Dimeric	Non-resp. Clds (Fig. 7)	7
HemQ†	3DTZ	Thermoplasma acidophilum: phylum Crenarchaeota	Pentameric; ligand-free	Group 1 HemQ (Fig. 7)	35
	1T0T	Geobacillus stearothermophilus: phylum Firmicutes	Pentameric; ligand-free	Group 2 HemQ (Fig. 7)	36
	1VDH	Thermus thermophilus: phylum Deinococcus-Thermus	Pentameric; ligand-free	Group 2 HemQ (Fig. 7)	37, 39
	4WWS	Listeria monocytogenes, phylum	Pentameric; heme-bound	Group 2 HemQ (Fig. 7)
OxdA	3W08	Pseudomonas chlororaphis: phylum Proteobacteria	Homodimer	--	27
	3A15, 3A16, 3A17, 3A18	Rhodoccus erythropolis: phylum Actinobacteria	Homodimer	--	27
IsdG	2ZDO, 1XBW, 1SQE, 3LGN, 3LGM	Staphylococcus aureus: phylum Firmicutes	Homodimer	--	42, 43, 45
	4NL5, 3HX9	Mycobacterium tuberculosis: phylum Actinobacteria	Homodimer	--	41, 44

^*Listed as to be published by the PDB.

^†Tentative functional assignment based on unpublished data (DuBois et al.) and informatics (Figure 7).