Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins

Milani, Mario; Pesce, Alessandra; Nardini, M.; Ouellet, Hugues; Ouellet, Yannick; Dewilde, Sylvia; Bocedi, Alessio; Ascenzi, Paolo; Guertin, Michel; Moëns, Luc

doi:10.1016/j.jinorgbio.2004.10.035

Cited by 121 publications

(151 citation statements)

References 79 publications

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“…To elucidate the potential residue(s) involved in the hexacoordinated conformation, we monitored selected key distances during the simulation. As reported for other Group II Hbs, the oxygen atom of TyrB10 was found to be close to the Fe(III) atom [16,20]. However, TyrCD1 was found to be even closer to the Fe(III) atom than TyrB10 (Fig.…”

Section: Molecular Dynamics Simulationssupporting

confidence: 71%

“…The sixth ligand is usually provided by the imidazole side chain of a His, normally present at the distal site of the heme pocket, and only a few examples have been reported where TyrB10 has been found to act as the sixth ligand at the iron site in the ferrous [55] and ferric states [16,20]. Indeed, the aminoacid sequence, the MD simulations, and the spectroscopic data of Ph-2/2HbO indicate that the distal ligands of the LS ferric form can be either TyrCD1 or TyrB10.…”

Section: Discussionmentioning

confidence: 99%

“…S2 of the ESM). These three positions are the most important for oxygen stabilization in this family of Hbs [16]. In contrast to Group I of 2/2 Hbs, the E7 and E11 positions are occupied by nonpolar aminoacid residues, Ile and Phe, respectively, precluding ligand stabilization by these two residues.…”

Section: Sequence Alignmentmentioning

confidence: 91%

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The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125

et al. 2010

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The genome of the cold-adapted bacterium Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct monomeric hemoglobins exhibiting a 2/2 a-helical fold. In the present work, one of these hemoglobins is studied by resonance Raman, electronic absorption and electronic paramagnetic resonance spectroscopies, kinetic measurements, and different bioinformatic approaches. It is the first cold-adapted bacterial hemoglobin to be characterized. The results indicate that this protein belongs to the 2/2 hemoglobin family, Group II, characterized by the presence of a tryptophanyl residue on the bottom of the heme distal pocket in position G8 and two tyrosyl residues (TyrCD1 and TyrB10). However, unlike other bacterial hemoglobins, the ferric state, in addition to the aquo hexacoordinated high-spin form, shows multiple hexacoordinated low-spin forms, where either TyrCD1 or TyrB10 can likely coordinate the iron. This is the first example in which both TyrCD1 and TyrB10 are proposed to be the residues that are alternatively involved in heme hexacoordination by endogenous ligands.

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Section: Molecular Dynamics Simulationssupporting

confidence: 71%

Section: Discussionmentioning

confidence: 99%

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The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125

et al. 2010

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“…2/2HbN displays a covalent bond linking HisH16 and the 2-vinyl group of the heme, that may modulate the reactivity of the heme group (10,11,21,22). Moreover, heme isomerism has been reported in some of the 2/2Hb crystal structures (23).…”

Section: Heme Proximal Site In 2/2hbsmentioning

confidence: 99%

“…Distal site polarity is a common property in 2/2 globins, although different residues may contribute to the architecture of the heme ligand surroundings in the three groups. In group I 2/2HbNs the hydrogen bonded network involves mostly residues at B10, E7, and E11 topological sites (23). For example, in Mt-2/2HbN a direct TyrB10-O 2 hydrogen bond occurs, stabilized by GlnE11 interacting with TyrB10 (9,24,26,31).…”

Section: Ligand Binding At the Heme Distal Sitementioning

confidence: 99%

Protein structure in the truncated (2/2) hemoglobin family

Pesce¹,

Nardini

Milani

et al. 2007

IUBMB Life

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The discovery of protein sequences belonging to the widespread 'truncated hemoglobin' family has been followed in the last few years by extensive analyses of their three‐dimensional structures. Truncated hemoglobins can be classified in three main groups, in light of their overall structural properties. The three groups adopt a 2‐on‐2 α‐helical sandwich fold, based on four main α‐helices of the classical 3‐on‐3 α‐helical sandwich found in vertebrate and invertebrate globins. Each of the three groups displays sequence and structure specific features. Among these, a protein matrix tunnel system is typical of group I, a Trp residue at the G8 topological site is conserved in groups II and III, and residue TyrB10 is almost invariant in the three groups. Despite sequence variability in the heme distal site region, a strongly intertwined, but varied, network of hydrogen bonds stabilizes the heme ligand in the three protein groups. Fine mechanisms of ligand recognition and stabilization may vary based on group‐specific distal site residues and on differing ligand diffusion pathways to the heme. Taken together, the structural considerations here presented underline that 'truncated hemoglobins' result from careful editing of the 3‐on‐3 α‐helical globin sandwich fold, rather than from simple 'truncation' events. Thus, '2/2Hb' appears the most proper term to concisely address this protein family.

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The Thermochemistry and Energetics of Organoiron Compounds

Liebman

Slayden

2014

Patai's Chemistry of Functional Groups

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The current study concerns the thermochemistry and energetics of organoiron compounds that contain an iron–carbon bond. The main quantities that are discussed are enthalpies of formation and bond energies. The chapter begins with the simplest binary iron carbides and then considers progressively larger neutral and ionic organic ligands. Within the context of small ligands, binding to iron as found in hemes and hemoglobin is discussed. The acidity and basicity of iron‐containing compounds is also included.

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Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins

Cited by 121 publications

References 79 publications

The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125

The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125

Protein structure in the truncated (2/2) hemoglobin family

The Thermochemistry and Energetics of Organoiron Compounds

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