Unusual Rocking Freedom of the Heme in the Hydrogen Sulfide-Binding Hemoglobin from <i>Lucina</i> <i>pectinata</i>

Cerda-Colón, José F.; Silfa, Eilyn; López‐Garriga, Juan

doi:10.1021/ja972654m

Cited by 66 publications

(72 citation statements)

References 27 publications

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“…It is worth noting that the high-frequency RR spectrum also reveals the presence of a 5cHS form at alkaline pH (m 3 1491 cm À1 ) ( Fig. 4D) at pH > 10 the H-bonding interactions with the propionyl groups (observed in the X-ray structure) are weakened [34]. Figures S2-S5 and Tables S2-S5 report the curve fitting analysis of the RR spectra shown in Fig.…”

Section: Spectroscopic Measurements In Solutionmentioning

confidence: 79%

Structural flexibility of the heme cavity in the cold‐adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

et al. 2015

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*These authors contributed equally to this workTruncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two a-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21A resolution) shows typical features of group-II truncated hemoglobins, namely the twoon-two a-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low Abbreviations 5c, penta-coordinated heme state; 6c, hexa-coordinated heme state; At-2/2HbO, TrHbII from Agrobacterium tumefaciens; Ath-2/2HbO,

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Section: Spectroscopic Measurements In Solutionmentioning

confidence: 79%

Structural flexibility of the heme cavity in the cold‐adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

et al. 2015

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“…The propionate bending mode in b-type CcmE, ␦(C ␤ C c C d ) 6,7 , is observed at 386, 384, and 380 cm Ϫ1 for the ferric, ferrous, and CO-bound forms, respectively; these values are higher than those of myoglobin (376, 370, 379 cm Ϫ1 , respectively) (19). Because the frequency of this band is correlated with the strength of the hydrogen bonds between the heme propionate groups and surrounding amino acids (21,22), the higher ␦(C ␤ C c C d ) 6 Fig. 4.…”

Section: Resultsmentioning

confidence: 96%

Dynamic Ligation Properties of the Escherichia coli Heme Chaperone CcmE to Non-covalently Bound Heme

Stevens

Uchida

Daltrop

et al. 2006

Journal of Biological Chemistry

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The cytochrome c maturation protein CcmE is an essential membrane-anchored heme chaperone involved in the post-translational covalent attachment of heme to c-type cytochromes in Gram-negative bacteria such as Escherichia coli. Previous in vitro studies have shown that CcmE can bind heme both covalently (via a histidine residue) and non-covalently. In this work we present results on the latter form of heme binding to a soluble form of CcmE. Examination of a number of site-directed mutants of E. coli CcmE by resonance Raman spectroscopy has identified ligands of the heme iron and provided insight into the initial steps of heme binding by CcmE before it binds the heme covalently. The heme binding histidine (His-130) appears to ligate the heme iron in the ferric oxidation state, but two other residues ligate the iron in the ferrous form, thereby freeing His-130 to undergo covalent attachment to a heme vinyl group. It appears that the heme ligation in the non-covalent form is different from that in the holo-form, suggesting that a change in ligation could act as a trigger for the formation of the covalent bond and showing the dynamic and oxidation state-sensitive ligation properties of CcmE.c-type cytochromes are proteins that contain covalently attached heme cofactors and are essential for the life of virtually all organisms. Cytochrome c in the mitochondria respiratory chain contains a single heme molecule, whereas many bacterial c-type cytochromes are found to contain many hemes; a Geobacter cytochrome c appears to contain 27 heme molecules (1). The heme is characteristically covalently attached to a CXXCH motif and allows the proteins to function in electron transfer and to catalyze a variety of reactions. The biogenesis of c-type cytochromes is a complex post-translational process that, in Gram-negative bacteria such as Escherichia coli, occurs in the periplasm. The heme attachment reaction appears to occur by very different pathways in different types of organisms; in humans, for example, a single protein called heme lyase is involved, whereas in E. coli at least ten proteins are essential for the process (2, 3). The latter system is known as the cytochrome c maturation (Ccm) 6 system and comprises the proteins CcmABCDEFGH, all of which are anchored to the cytoplasmic membrane or integral to it (4) as indicated in Fig. 1a. The membrane-anchored protein CcmE has been described as a heme chaperone and binds heme covalently in the bacterial periplasm before the heme is transferred to apocytochromes (5). Unusually, the protein binds heme covalently via a single histidine residue, as opposed to the binding of heme to two cysteine residues in cytochromes c. It is not known how heme is transported into the periplasm from its site of synthesis in the cytoplasm, but it is known that the protein CcmC is essential for the provision of heme to CcmE (6). The protein CcmF has been shown to form a complex with CcmE (7), but its function remains unknown, as do the precise roles of the other Ccm proteins. Recently, CcmD was sho...

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“…The ␦(C ␤ C c C d ) mode of the O 2 -bound Ec DOSH was also observed at 384 cm Ϫ1 (not shown). The frequency of ␦(C ␤ C c C d ) is indicative of hydrogen bonding between the heme propionates and the surrounding residues (37). In Mb, the heme 7-propionate constitutes a hydrogen bond with His-97 and Ser-92, and the ␦(C ␤ C c C d ) mode appears at 376 cm Ϫ1 .…”

Section: Interactions Between Heme-bound Ligand and Distalmentioning

confidence: 99%

Roles of Arg-97 and Phe-113 in Regulation of Distal Ligand Binding to Heme in the Sensor Domain of Ec DOS Protein

El-Mashtoly

Nakashima²,

Tanaka

et al. 2008

Journal of Biological Chemistry

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The direct oxygen sensor protein isolated from Escherichia coli (Ec DOS) is a heme-based signal transducer protein responsible for phosphodiesterase (PDE) activity. Binding of O 2 , CO, or NO to a reduced heme significantly enhances the PDE activity toward 3,5-cyclic diguanylic acid. We report stationary and time-resolved resonance Raman spectra of the wild-type and several mutants (Glu-93 3 Ile, Met-95 3 Ala, Arg-97 3 Ile, Arg-97 3 Ala, Arg-97 3 Glu, Phe-113 3 Leu, and Phe-113 3 Thr) of the heme-containing PAS domain of Ec DOS. For the CO-and NO-bound forms, both the hydrogen-bonded and nonhydrogen-bonded conformations were found, and in the former Heme-based sensors are a class of enzymes that regulates the enzymatic activities and DNA binding in response to the presence of diatomic gas molecules CO, NO, or O 2 (1-6). The direct oxygen sensor from Escherichia coli (Ec DOS) 4 is a hemebased signal transducer protein responsible for phosphodiesterase (PDE) activity (7,8). The Ec DOS is composed of a C-terminal PDE catalytic domain and the N-terminal hemecontaining domain. The latter is a prototypical PAS domain, which is a ubiquitous protein sensory domain found in all kingdoms (9), and has a conserved ␣/␤ folds consisting of ϳ147 residues (10, 11). The Ec DOS protein has a PDE activity specific to 3Ј,5Ј-cyclic diguanylic acid (12, 13), and the binding of O 2 , CO, or NO to the reduced heme significantly enhances the PDE activity (14, 15). Thus, Ec DOS is a novel gas-sensor enzyme that has unprecedented ability to be activated by different gas molecules. Because the CO and NO concentrations in the cells are very low (nanomolar), it is likely that Ec DOS is predominantly an oxygen sensor enzyme whereby catalysis is regulated in response to the micromolar O 2 level (16). It is believed that the structural changes in the heme vicinity caused by ligand binding to the heme provide the initial event in the gas sensing, followed by intramolecular signal transduction from the heme to the functional domain, and thus regulating the PDE activity. Fig. 1 illustrates the crystal structure of the truncated heme sensor domain (Ec DOSH) of Ec DOS protein (10). In the reduced form (Fig. 1A), Met-95 and His-77 are the heme axial ligands in the distal and proximal sides, respectively, and Met-95 forms a hydrogen bond with heme 7-propionate. Upon O 2 binding to the reduced heme, Met-95 is replaced by O 2 and heme 7-propionate forms a hydrogen bond with Arg-97 instead of Met-95. This stabilizes the heme-coordinated O 2 (Fig. 1B). Thus, the replacement of a distal axial ligand from Met-95 to O 2 perturbs the heme 7-propionate hydrogen bonding network, resulting in large conformational changes in the FG loop (10). On the other hand, the role of other distal residues (Fig. 1) and the heme 7-propionate hydrogen bonding network are not clear in the CO-or NO-sensing mechanism.To understand the gas-sensing mechanism of Ec DOS, it is essential to determine the changes in the heme and surrounding structures caused by distal ligand binding/di...

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Unusual Rocking Freedom of the Heme in the Hydrogen Sulfide-Binding Hemoglobin from Lucina pectinata

Cited by 66 publications

References 27 publications

Structural flexibility of the heme cavity in the cold‐adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

Structural flexibility of the heme cavity in the cold‐adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

Dynamic Ligation Properties of the Escherichia coli Heme Chaperone CcmE to Non-covalently Bound Heme

Roles of Arg-97 and Phe-113 in Regulation of Distal Ligand Binding to Heme in the Sensor Domain of Ec DOS Protein

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