A 2.0-Å structure of the blue copper protein (cupredoxin) from Alcaligenes faecalis S-6

Adman, Elinor T.; Turley, S.; Bramson, R; Petratos, Kyriacos; Banner, David W.; Tsernoglou, Demetrius; Beppu, Teruhiko; Watanabe, Haruyuki

doi:10.1016/s0021-9258(17)31227-9

Cited by 97 publications

(45 citation statements)

References 35 publications

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“…The crystallographic structures of pseudoazurine precursor (Adman et al, 1989) and plastocyanin (Guss and Freeman, 1983) were structurally superimposed and the aligned sequences from the tertiary structures were compared with the alignment by the double window approach. The amino acid sequences of five small copper-containing proteins [pseudoazurine, pseudoazurine precursor (cupredoxin), plastocyanin, auracyanin, and rusticyanin from Thiobacillusferroxidants] (Nunzi et al, 1993), were used in the sequence analysis and modeling with the sequences of a,-, a3-, a4-, ,I-, -y-, and S-subunits of the nAChR.…”

Section: Modeling Of Tertiary Structuresmentioning

confidence: 99%

“…Regions of identity are superimposed for these 105 and 143 amino acid proteins (cf. Guss and Freeman, 1983;Adman et al, 1989). Single letter codes are shown for the positions of aminoand carboxyl-terminal amino acids in the alignment.…”

Section: S106 Y115mentioning

confidence: 99%

“…Four insertions in the a,-subunit were included: 1) a loop between residues 85 and 96 oriented to the (+) face according to labeling of aY93, 2) a loop between residues 104 and 111 oriented to the (-) face according to the conotoxin Ml determinant ,yS1l1/6Y113, 3) a loop between residues 67 and 76 ori-Biophysical Journal *1 FIGURE 7 Superimposition of ribbon diagrams of pseudoazurin (PAZI) (black) and the a-subunit of nicotinic acetylcholine receptor (gray). Shown are the a-carbon backbone of PAZI from the x-ray crystallographic structure (Adman et al, 1989) from residues 41 to 143 and the modeled structure of the a-subunit of the nAChR from the residues 39 to 164. Specific residues in the nAChR a-subunit are denoted by the black rings.…”

Section: Structural Model Of the Extracellular Domain Of Nachr Subunitsmentioning

confidence: 99%

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A model of the nicotinic receptor extracellular domain based on sequence identity and residue location

Tsigelny

Sugiyama

Sine

et al. 1997

Biophysical Journal

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We have modeled the extracellular domains of individual subunits (amino acids 31-200) in the nicotinic acetylcholine receptor using sequence homology with copper binding proteins of known crystal structure, plastocyanin and pseudoazurin, and data from recent site-specific mutagenesis, antibody mapping, and site-directed labelling studies. These data formed an initial model that was refined using molecular dynamics and mechanics as well as electrostatic and solvation energy calculations. The sequences between residues 31 and 164 in the alpha 1-subunit and corresponding residues in homologous receptor subunits show similarity with the core sequence of the cation binding site in plastocyanin and pseudoazurin, a region in the template proteins characterized by multiple hairpin loops. In addition to defining the subunit interfaces that comprise the site for agonist and competitive antagonist binding in more detail, the findings show that negatively charged residues cluster in domains arranged to diminish electrostatic free energy of the complex. Electrostatic factors also appear to distinguish the ligand binding interfaces, alpha gamma and alpha delta, from the other three interfaces on the pentameric receptor.

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Section: Modeling Of Tertiary Structuresmentioning

confidence: 99%

Section: S106 Y115mentioning

confidence: 99%

Section: Structural Model Of the Extracellular Domain Of Nachr Subunitsmentioning

confidence: 99%

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A model of the nicotinic receptor extracellular domain based on sequence identity and residue location

Tsigelny

Sugiyama

Sine

et al. 1997

Biophysical Journal

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“…The cupredoxins for which high-resolution X-ray crystal structures are available comprise poplar (Populus nigra) plastocyanin (Guss & Freeman, 1983), Oleander nerium plastocyanin (Tong, 1991), algal (Enteromorpha prolifera) plastocyanin (Collyer et al, 1990), Alcaligenes denitrificans azurin (Baker, 1988), cucumber basic blue protein (Guss et al, 1988), and Alcaligenes faecalis pseudoazurin (Petratos et al, 1988;Adman et al, 1989). There is also a cupredoxin-type domain in the multinuclear copper protein, zucchini ascorbate oxidase (Messerschmidt et al, 1989), and the existence of similar domains in two other multinuclear copper proteins, lacease and ceruloplasmin, has been inferred from the primary structures (Messerschmidt & Huber, 1990).…”

mentioning

confidence: 99%

Resonance Raman spectra of plastocyanin and pseudoazurin: evidence for conserved cysteine ligand conformations in cupredoxins (blue copper proteins)

Han

Adman²,

Beppu³

et al. 1991

Biochemistry

108

139

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New resonance Raman (RR) spectra at 15 K are reported for poplar (Populus nigra) and oleander (Oleander nerium) plastocyanins and for Alcaligenes faecalis pseudoazurin. The spectra are compared with those of other blue copper proteins (cupredoxins). In all cases, nine or more vibrational modes between 330 and 460 cm-1 can be assigned to a coupling of the Cu-S(Cys) stretch with Cys ligand deformations. The fact that these vibrations occur at a relatively constant set of frequencies is testimony to the highly conserved ground-state structure of the Cu-Cys moiety. Shifts of the vibrational modes by 1-3 cm-1 upon deuterium exchange can be correlated with N-H...S hydrogen bonds from the protein backbone to the sulfur of the Cys ligand. There is marked variability in the intensities of these Cys-related vibrations, such that each class of cupredoxin has its own pattern of RR intensities. For example, plastocyanins from poplar, oleander, French bean, and spinach have their most intense feature at approximately 425 cm-1; azurins show greatest intensity at approximately 410 cm-1, stellacyanin and ascorbate oxidase at approximately 385 cm-1, and nitrite reductase at approximately 360 cm-1. These variable intensity patterns are related to differences in the electronic excited-state structures. We propose that they have a basis in the protein environment of the copper-cysteinate chromophore. A further insight into the vibrational spectra is provided by the structures of the six cupredoxins for which crystallographic refinements at high resolution are available (plastocyanins from P. nigra, O. nerium, and Enteromorpha prolifera, pseudoazurin from A. faecalis, azurin from Alcaligenes denitrificans, and cucumber basic blue protein). The average of the Cu-S(Cys) bond lengths is 2.12 +/- 0.05 A. Since the observed range of bond lengths falls within the precision of the determinations, this variation is considered insignificant. The Cys ligand dihedral angles are also highly conserved. Cu-S gamma-C beta-C alpha is always near -170 degrees and S gamma-C beta-C alpha-N near 170 degrees. As a result, the Cu-S gamma bond is coplanar with the Cys side-chain atoms and part of the polypeptide backbone. The coplanarity accounts for the extensive coupling of Cu-S stretching and Cys deformation modes as seen in the RR spectrum. The conservation of this copper-cysteinate conformation in cupredoxins may indicate a favored pathway for electron transfer.

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“…The sequence homologies of plastocyanin, pseudoazurin, amicyanin, and halocyanin are reflected in the similarities of their tertiary structures and in the crystal structures of plastocyanin [22], pseudoazurin [76,77] and amicyanin [20,78]. The peptide chains of plastocyanin and pseudoazurin consist of eight, and that of amicyanin nine, fl-sheets which are connected by loops.…”

Section: The Plastocyanin Familymentioning

confidence: 99%

Evolutionary aspects of copper binding centers in copper proteins

Abolmaali

Taylor

Weser

Structure and Bonding

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A great number of active centers in proteins and enzymes contain transition metals. Each metal imposes specific catalytic properties on the protein which could not be achieved when employing a different metal. The special role and characteristic reactivity of coordinated copper is illustrated by looking at the evolutionary aspects of copper proteins. The evolution of copper-binding sites is closely linked to that of copper proteins. Copper centers have evolved according to various principles, similar to the evolutionary development of proteins and enzymes. Three basic principles may be observed: the copper-binding centers of metallothioneins and type 1 copper centers developed in non-metal proteins; the transformation of the metal-binding centers of iron or manganese proteins led to the development of the type 2 copper centers; and the trinuclear copper-binding centers of the blue oxidases were formed by alterations and recombinations of type 1 copper centers. Simple, although as yet unknown, mononuclear copper centers gave rise to the type 3 copper-binding sites of the hemocyanins and tyrosinases, as well as to the Cu A-and CUB-centers of the cytochrome oxidases and N20reductase. According to this assignment, copper proteins containing either type 1 copper, type 3 copper, CUA-centers, or CUB-centers share a common ancestor. They developed at least in part by divergent evolution. Type 2 copper proteins are the products of convergent evolution and, consequently, show little or no phylogenetic homology.

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A 2.0-Å structure of the blue copper protein (cupredoxin) from Alcaligenes faecalis S-6

Cited by 97 publications

References 35 publications

A model of the nicotinic receptor extracellular domain based on sequence identity and residue location

A model of the nicotinic receptor extracellular domain based on sequence identity and residue location

Resonance Raman spectra of plastocyanin and pseudoazurin: evidence for conserved cysteine ligand conformations in cupredoxins (blue copper proteins)

Evolutionary aspects of copper binding centers in copper proteins

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