Structural hierarchy in erythrocruorin, the giant respiratory assemblage of annelids

Royer, William E.; Strand, Kristen; Heel, Marin van; Hendrickson, Wayne A.

doi:10.1073/pnas.97.13.7107

Cited by 98 publications

(89 citation statements)

References 31 publications

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“…The direct observation of dodecamer globin subassemblies by ESI-TOF-MS in Nephelopsis Hb provides concrete evidence for their existence within these giant heteromultimeric complexes in solution. This result is in full accord with the "bracelet" model of the quaternary structure of HBL Hbs proposed earlier [20] and strongly supported by the recent low-resolution crystal structure of Lumbricus Hb [21]: An HBL complex of 12 dodecamer subassemblies tethered to 36 linker chains. Based on this model the expected mass of Nephelopsis Hb would be 208.33 ϫ 12 ϩ 24.95 ϫ 36 ϭ 3398 kDa , well within the observed range of masses of HBL Hbs [4].…”

Section: Resultssupporting

confidence: 90%

An electrospray ionization mass spectrometric study of the subunit structure of the giant hemoglobin from the leech Nephelopsis oscura

Green

Vinogradov

2004

J. Am. Soc. Mass Spectrom.

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The subunit structure of the giant, extracellular hexagonal bilayer (HBL) hemoglobin (Hb) from the leech Nephelopsis oscura was investigated by electrospray ionization mass spectrometry (ESI-MS) employing a maximum entropy deconvolution of its complex, multiply charged ESI spectra. The denatured unreduced Hb consisted of three monomer globin chains These giant complexes were found to have masses of ϳ3500 kDa and to consist of two types of polypeptide chains: heme-containing 16 -17 kDa globin chains and non-globin, linker chains of 24 -32 kDa containing 9 to 12 cysteines [4]. The amino acid sequences of the globin chains are clearly related to vertebrate and invertebrate globins [5] and they form disulfide-bonded dimer, trimer and tetramer subunits as well as noncovalent subassemblies, ranging from dimer to dodecamer [4].Over the last decade, ESI-MS has been shown to be the method of choice for the characterization of proteins [6,7] by providing highly accurate masses. In particular, in the case of heteromultimeric protein complexes, as exemplified by the HBL Hbs, ESI-MS provides an exquisitely accurate enumeration of the constituent chains and covalently bonded subunits, as well as a quantitative determination of free and disulfidebonded Cys residues [8]. Furthermore, the combination of nanoflow electrospray and time-of-flight (TOF) mass analyzers has recently allowed the investigation of the quaternary structure of large noncovalent protein complexes [9].We describe here the results of ESI-MS and ESI-TOF-MS studies of the polypeptide chain and subunit composition and noncovalent subassemblies of the HBL Hb from the leech Nephelopsis oscura.

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Section: Resultssupporting

confidence: 90%

An electrospray ionization mass spectrometric study of the subunit structure of the giant hemoglobin from the leech Nephelopsis oscura

Green

Vinogradov

2004

J. Am. Soc. Mass Spectrom.

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“…Since 1996 a significant effort has been devoted by several laboratories to elucidate in more detail the arrangements between the subunits from the structural point of view to better understand the oxygenation of this giant hemoglobin. The three most important contributions in this research are associated with the mass spectrometry determination of the molecular masses of all subunits (3), to the three-dimensional reconstructions at a low resolution of 35 Å obtained by cryoelectron microscopy (1) and which were able to give results on the shape and dimensions of the whole protein, and, finally, to the recently reported crystal structure of Hb of L. terrestris obtained at a resolution of 5.5 Å, which allowed us to establish a complicated hierarchy of overall D6 symmetry, in agreement with previous findings, and local D3 symmetry for smaller subunits as well as the location of the linker chains in the whole oligomeric structure (5).…”

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confidence: 74%

Small Angle X-ray Scattering (SAXS) Study of the Extracellular Hemoglobin of Glossoscolex paulistus

Gelamo

Itri

Tabak

2004

Journal of Biological Chemistry

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pH effects on the oligomeric structure of giant Glossoscolex paulistus extracellular hemoglobin in the oxyand met-forms have been studied as well as effects of the addition of anionic sodium dodecyl sulfate surfactant. A radius of gyration of 110 Å is observed for a macromolecule. At 2 mM surfactant, the radius of gyration diminishes slightly for the oxy-form. However, the extrapolated initial scattering intensity (I(0)) decreases a factor of 2.5, indicating protein dissociation. At 20 mM surfactant, further I(0) decrease is observed, with a reduction of radius of gyration to approximately 30 Å consistent with dissociation into smaller subunits. At pH 9.0, the scattering curves are similar to that obtained for the protein in the presence of 20 mM surfactant at pH 7.0. A radius of gyration of approximately 35 Å shows that the giant hemoglobin dissociation into small subunits also occurs at alkaline pH. From the I(0) value, one can suggest that the tetramer is the main scatter at pH 9.0. At pH 7.0, the met-form dissociates to a larger extent at 2 mM surfactant as compared with the oxy-form, and the main scatters seem to be the 1/12 subunit. At pH 9.0, for the oxy-form, the addition of surfactant does not modify the scattering curve and a radius of gyration approximately 30 Å is obtained, while for the met-form some kind of aggregation is observed. Our results give support to conclude that the iron oxidation state is an important factor modulating the oligomeric dissociation.Annelid extracellular hemoglobins are giant molecules that have a characteristic hexagonal bilayer appearence in electron micrographs, high cooperativity of oxygen binding, and low iron and heme contents (1-4). The hemoglobin of the earthworm Lumbricus terrestris (HbLt) 1 is the most extensively studied annelid hemoglobin. It consists of about 180 polypeptide chains in an arrangement of two heme-containing subunits (monomer M and disulfide-bonded trimer T) and non-globin linker subunits with molecular masses in the range 24 -32 kDa. A model of quaternary structure (bracelet model) explains the properties and subunit structure of HbLt: three copies of monomer subunit and three copies of the trimer subunit form a dodecamer subunit, (abcd) 3 of about 200 kDa. Twelve such complexes of heme-containing chains are linked together by 36 heme-deficient linker chains to provide the total mass of about 3500 kDa. The 1/12 subunit of the whole protein is associated then to (abc) 3 d 3 L 3 , where L stands for the linker chains. Since 1996 a significant effort has been devoted by several laboratories to elucidate in more detail the arrangements between the subunits from the structural point of view to better understand the oxygenation of this giant hemoglobin. The three most important contributions in this research are associated with the mass spectrometry determination of the molecular masses of all subunits (3), to the three-dimensional reconstructions at a low resolution of 35 Å obtained by cryoelectron microscopy (1) and which were able to give results o...

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“…The first consists of homologous proteins with different quaternary structures, such as globins (49) and lectins (50). These proteins have conserved tertiary structures; however, utilizing different types of protein contacts, they can assemble into a variety of quaternary states, from dimers to oligomers containing as many as 144 subunits as in the case of Lumbricus terrestris erythrocruorin (51). The second category involves transient or reversible domain interactions.…”

Section: Resultsmentioning

confidence: 99%

Structure of the Mouse Peptide N-Glycanase-HR23 Complex Suggests Co-evolution of the Endoplasmic Reticulum-associated Degradation and DNA Repair Pathways

Zhao

Zhou

Wang

et al. 2006

Journal of Biological Chemistry

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Peptide N-glycanase removes N-linked oligosaccharides from misfolded glycoproteins as part of the endoplasmic reticulum-associated degradation pathway. This process involves the formation of a tight complex of peptide N-glycanase with Rad23 in yeast and the orthologous HR23 proteins in mammals. In addition to its function in endoplasmic reticulum-associated degradation, HR23 is also involved in DNA repair, where it plays an important role in damage recognition in complex with the xeroderma pigmentosum group C protein. To characterize the dual role of HR23, we have determined the high resolution crystal structure of the mouse peptide N-glycanase catalytic core in complex with the xeroderma pigmentosum group C binding domain from HR23B. Peptide N-glycanase features a large cleft between its catalytic cysteine protease core and zinc binding domain. Opposite the zinc binding domain is the HR23B-interacting region, and surprisingly, the complex interface is fundamentally different from the orthologous yeast peptide N-glycanase-Rad23 complex. Different regions on both proteins are involved in complex formation, revealing an amazing degree of divergence in the interaction between two highly homologous proteins. Furthermore, the mouse peptide N-glycanase-HR23B complex mimics the interaction between xeroderma pigmentosum group C and HR23B, thereby providing a first structural model of how the two proteins interact within the nucleotide excision repair cascade in higher eukaryotes. The different interaction interfaces of the xeroderma pigmentosum group C binding domains in yeast and mammals suggest a co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways.Degradation of misfolded and misassembled proteins is essential for homeostasis and cell growth. In the endoplasmic reticulum (ER) 2 a quality control system sorts proteins on the basis of their conformation (1).Proteins that fail to mature in the ER are retro-translocated into the cytosol, polyubiquitinated, and targeted to the proteasome for degradation as part of the ER-associated degradation pathway (2). Defects in the ER-associated degradation system have been associated with many diseases including ␣-1 antitrypsin deficiency, cystic fibrosis, neurodegenerative disorders, tyrosinase deficiency, and cancer (3-6).Most of the misfolded glycoproteins are deglycosylated by a cytosolic peptide-N-glycanase (PNGase) activity before proteasomal degradation (7,8). PNGase hydrolyzes the ␤-aspartylglycosylamine bond of N-linked glycoproteins, which facilitates their degradation by the proteasome (9). PNGase is highly conserved from yeast to human, supporting its functional significance. In addition to the catalytic core, in higher eukaryotes PNGase contains one additional domain each at the N and C terminus, which may function as binding partners for other proteins (10).PNGase closely associates with the proteasome by either directly binding to components of the proteasome or through its interaction with HR23A/HR23B, the mammalian homologs of Ra...

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Structural hierarchy in erythrocruorin, the giant respiratory assemblage of annelids

Cited by 98 publications

References 31 publications

An electrospray ionization mass spectrometric study of the subunit structure of the giant hemoglobin from the leech Nephelopsis oscura

An electrospray ionization mass spectrometric study of the subunit structure of the giant hemoglobin from the leech Nephelopsis oscura

Small Angle X-ray Scattering (SAXS) Study of the Extracellular Hemoglobin of Glossoscolex paulistus

Structure of the Mouse Peptide N-Glycanase-HR23 Complex Suggests Co-evolution of the Endoplasmic Reticulum-associated Degradation and DNA Repair Pathways

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