The structure of plastocyanin from the cyanobacterium <i>Phormidium laminosum</i>

Bond, Charles S.; Bendall, Derek S.; Freeman, H.C.; Guss, J.M.; Howe, Christopher J.; Wagner, Michael J.; Wilce, Matthew Charles James

doi:10.1107/s0907444998012074

Cited by 45 publications

(57 citation statements)

References 26 publications

(18 reference statements)

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“…8). The template for the Cu 2+ –binding protein, human ceruloplasmin (PDB ID∶1KCW) [34], almost perfectly aligned with the Cu 2+ –binding site in the A chain of plastocyanin (PDBID∶1BAW) [35] (Fig. 9), although a few FP metal ion–binding residues were also identified.…”

Section: Resultsmentioning

confidence: 92%

Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

et al. 2012

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The structure of a protein determines its function and its interactions with other factors. Regions of proteins that interact with ligands, substrates, and/or other proteins, tend to be conserved both in sequence and structure, and the residues involved are usually in close spatial proximity. More than 70,000 protein structures are currently found in the Protein Data Bank, and approximately one-third contain metal ions essential for function. Identifying and characterizing metal ion–binding sites experimentally is time-consuming and costly. Many computational methods have been developed to identify metal ion–binding sites, and most use only sequence information. For the work reported herein, we developed a method that uses sequence and structural information to predict the residues in metal ion–binding sites. Six types of metal ion–binding templates– those involving Ca2+, Cu2+, Fe3+, Mg2+, Mn2+, and Zn2+–were constructed using the residues within 3.5 Å of the center of the metal ion. Using the fragment transformation method, we then compared known metal ion–binding sites with the templates to assess the accuracy of our method. Our method achieved an overall 94.6 % accuracy with a true positive rate of 60.5 % at a 5 % false positive rate and therefore constitutes a significant improvement in metal-binding site prediction.

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Section: Resultsmentioning

confidence: 92%

Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

et al. 2012

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“…MD calculations were performed on the structures of Pc [33] and the soluble fragment of Cf [34] from Phormidium, deposited at PDB [35] (access codes 1BAW and 1CI3, respectively) and two of the 10 best NMR structures of their complex [29] (gently provided by Dr. M. Ubbink). Simulations were carried out by using AMBER 8.0 [36] under the AMBER 95 force field [37] in a Dell PowerEdge workstation.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Electrostatic strain and concerted motions in the transient complex between plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum

Dı́az-Moreno¹,

Muñoz-López²,

Frutos-Beltrán³

et al. 2009

Bioelectrochemistry

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Many fleeting macromolecular interactions, like those being involved in electron transport, are essential in biology. However, little is known about the behaviour of the partners and their dynamics within their short-lived complex. To tackle such issue, we have performed molecular dynamics simulations on an electron transfer complex formed by plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Besides simulations of the isolated partners, two independent trajectories of the complex were calculated, starting from the two different conformations in the NMR ensemble. The first one leads to a more stable ensemble with a shorter distance between the metal sites of the two partners. The second experiences a significant drift of the complex conformation. Analyses of the distinct calculations show that the conformation of cytochrome f is strained upon binding of its partner, and relaxes upon its release. Interestingly, the principal component analysis of the trajectories indicates that plastocyanin displays a concerted motion with the small domain of cytochrome f that can be attributed to electrostatic interactions between the two proteins.

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“…plastocyanin 44 (PDB: 1BAW 42 ), a plastocyanin that is, a close homologue to A.v. plastocyanin (66% sequence identity).…”

Section: Agreement Of the Observed 1 H Pseudocontact Shifts With The mentioning

confidence: 99%

“…Superposition of the crystal structure of P.l. plastocyanin 44 (red trace) and the solution structure of A. v. plastocyanin 22 (green trace). The blue spheres indicate the copper ions.…”

Section: Agreement Of the Observed 1 H Pseudocontact Shifts With The mentioning

confidence: 99%

“…19,20 The 1 H pseudocontact shifts obtained using the Cd 2C -substituted protein as the diamagnetic reference were included as restraints in the structure refinement by plastocyanin. 44 The calculated pseudocontact shifts were obtained from the crystal structure of P.l. plastocyanin, and the g-tensor parameters, derived as described in the text using Eqn (2), the crystal structure and the experimental pseudocontact shifts.…”

Section: Structure Refinementmentioning

confidence: 99%

See 1 more Smart Citation

On the use of pseudocontact shifts in the structure determination of metalloproteins

Jensen

Hansen

Ayna

et al. 2006

Magnetic Reson in Chemistry

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The utility of pseudocontact shifts in the structure refinement of metalloproteins has been evaluated using a native, paramagnetic Cu 2+ metalloprotein, plastocyanin from Anabaena variabilis (A.v.), as a model protein. First, the possibility of detecting signals of nuclei spatially close to the paramagnetic metal ion is investigated using the WEFT pulse sequence in combination with the conventional TOCSY and 1 H-15 N HSQC sequences. Second, the importance of the electrical charge of the metal ion for the determination of correct pseudocontact shifts from the obtained chemical shifts is evaluated. Thus, using both the Cu + plastocyanin and Cd 2+ -substituted plastocyanin as the diamagnetic references, it is found that the Cd 2+ -substituted protein with the same electrical charge of the metal ion as the paramagnetic Cu 2+ plastocyanin provides the most appropriate diamagnetic reference signals. Third, it is found that reliable pseudocontact shifts cannot be obtained from the chemical shifts of the 15 N nuclei in plastocyanin, most likely because these shifts are highly dependent on even minor differences in the structure of the paramagnetic and diamagnetic proteins. Finally, the quality of the obtained 1 H pseudocontact shifts, as well as the possibility of improving the accuracy of the obtained structure, is demonstrated by incorporating the shifts as restraints in a refinement of the solution structure of A.v. plastocyanin. It is found that incorporation of the pseudocontact shifts enhances the precision of the structure in regions with only few NOE restraints and improves the accuracy of the overall structure.

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The structure of plastocyanin from the cyanobacterium Phormidium laminosum

Cited by 45 publications

References 26 publications

Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

Electrostatic strain and concerted motions in the transient complex between plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum

On the use of pseudocontact shifts in the structure determination of metalloproteins

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