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{{Template:Sandbox Reserved Wayne Decatur}}
'''Plastocyanin from a Green Alga, Enteromorpha prolifera'''
=Molecular Visualization Problem #3=
by: Karen Plevock, Chris Meaden, Alyssa Gable
==IMAGES==


<applet load='1d66' size='250' frame='true' align='left' scene='Sandbox_142/Figure1/1' caption='2KTQ' /> <applet load='1d66' size='250' frame='true' align='left' scene='Sandbox_142/Distance_oxygen_oxygen3ktq/2' caption='3KTQ distance between oxygen atom of residue 671 and incoming nucleotide' /> <applet load='1d66' size='250' frame='true' align='left' scene='Sandbox_142/Distance_oxygen_oxygen_2ktq/1' caption='2KTQ distance between oxygen atom of residue 671 and incoming nucleotide' />
Please do NOT make changes to this sandbox. This sandbox is currently reserved, ESBS for use of Protopedia project. Bichelberger and Raphalen.
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==WORKSHEET PROBLEMS==
<Structure load='7PCY' size='500' frame='true' align='right' caption='Protein name : plastocyanin; Organism : Enteromorpha prolifera; Taxonomie : Eukaryota › Viridiplantae › Chlorophyta › Ulvophyceae › Ulvales › Ulvaceae › Ulva; Resolution : 1.80 &Aring;; Poids : 10,500 D' scene='Insert optional scene name here' | left />
==<b>Part I</b>==
===<b>Page 1:</b>===
<br>-How many polypeptide and polynucleotide chains are on the screen?
<b>3</b>
<br>-Are there nucleic acid, protein, or both?
<b>Both</b>
<br>-If nucleic acid is present, what type of nucleic acid?
<b>DNA</b>
<br>-How many chains of protein make up this enzyme?
<b>1</b>
<br>-How many total residues of each chain are actually visible on the screen?
<br><b>Chain A=538</b>
<br><b>Chain B=12</b>
<br><b>Chain D=13</b>


===<b>Page 2:</b>===
<br>-What is the approximate molecular weight of the polypeptide chain visible on the screen?
<br><b>(538 residues)x(110 daltons/residue)=59.2kD</b>


<br>-What is the pdb identification code of this structure?
=='''Overview'''==
<b>2KTQ</b>
<br>-What does the pdb file associtaed with this structure say the structure is?
<b>Open ternary complex of large fragment of DNA polymerase I from Thermus aquaticus.</b>
<br>-Was this structure solved with NMR or X-Ray crystallography?
<b>X-Ray crystallography</b>
<br>-What is the resolution of this structure?
<b>2.3 Angstroms</b>
<br>-What organism is the native biological source of the enzyme in the structure?
<b>Thermus Aquaticus.</b>
<br>-What very general term describes that ranges of temperatures that native organism prefers?<b> high temperatures</b>
<br>-What scientific term is used to broadly classify organisms showing a preference for this temperature range?<b> thermophilic</b>
<br>-In what popular lab procedure is this enzyme most commonly used? What is one reason this enzyme is a good choice for this common lab procedure? <b>PCR. DNA polI of other organisms would denature at the repeated high temperatures required for the melting apart of DNA strands during PCR reactions.</b>
<br>-<b>At what pH does the polypeptide chain visible on the screen have a net charge of zero?</b>


<br>-Which chain is the template? <b>D</b>
Plastocyanin is an important copper-containing protein involved in photosynthesis by all  higher plants and some algae namely by Enteromorpha prolifera. Plastocyanin extracted from this alga, was the first algal blue copper protein characterized by X-ray crystallography and one of the best characterized electron transfer protein of the photosynthetic apparatus. This protein was intensively studied between 1981 and 1994 because of these particular spectroscopic and electronic properties. The high resolution structural analysis  by molecular replacement in 1989 provided an accurate description of the structure of this protein. [http://www.sciencedirect.com/science/article/pii/002228369090269R J. Mol. Biol.] Plastocyanin is an electron donor localized in the intern membrane of thylakoïd in chloroplast. This is a monomeric protein with a single polypeptide chain of 98 amino acids and one copper atom. The molecular weight of plastocyanin is around 10,500 Daltons.
<br>-Which chain is the primer? <b>B</b>


<br>-<b>In order to get a homogenous population of a paused complex of a functional polymerase, one approach is to leave out at least one of the four nucleotides so that it will stop when it gets to the point that nucleotide is needed. Was that done for this structure? No</b>
=='''Structure'''==


===<b> Page 3: </b>===
===Residue distribution===
<br>-The primer chain ends in a nucleotide not defined as G,A,T or C because it is unusual. What is unusual about it? <b> There is no reactive OH group to incorporate another nucleotide at the 3' end.</b>
<br>- What is a more general, chemically descriptive name for such types of nucleotides? <b> dideoxyribonucleotide</b>
Plastocyanin extracted from a Green Alga, Enteromorpha prolifera, has a '''β-sandwich structure''' as  a slightly flattened cylinder with approximate dimensions  40 Å × 32 Å × 28 Å.          [http://www.nature.com/nature/journal/v272/n5651/abs/272319a0.html  Nature] This β-sandwich  is composed of two β-sheets (I and II) separated by a hydrophobic core. Turns on the two β-sheets occur between residues 42 to 45 and 47 to 50.
<br>-Noting the unusual feature, why has the enzyme not added the incoming nucleotide to the chain?<b> Th OH group is needed to provide energy to form a phosphodiester bond.</b>
Seven strands (1 to 4 and 6 to 8) of the polypeptide backbone have substantial β character and contribute to the β-sheets. The 5 strand has no β character and formed a helical segment.
<br>-Name a common lab procedure that relies on the use of such a type of nucleotide. <b>Sequencing</b>
The symmetry of this molecule related on an van der Waals’ bond on the northern loop between strands 3 and 4 the side-chain of Pro36  which contacts Gln 68.
<br>-Can you tell what base is on the 3' end of the primer chain? <b>C</b>
This plastocyanin includes important '''“acidic patch”''' which is localized between residues 59 to 61 and 42 to 45. [http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1986.tb09694.x/pdf Eur.J. Biochem.]
<br>-What is the sequence of each strand of nucleic acid shown? <br><b>Chain B 5' GACCACGGCGC*DOC 3'<br>Chain D 5' GGGCGCCGTGGTC 3' </b>
This acidic patch is significant in electron transfer namely facilitating electrostatic recognition of her redox partner( see Role in Photosynthesis).
<br>-Where is the oncoming nucleotide relative to the primer strand? <b> It will be incorporated at the 3' end of the primer strand. It will be a C base pairing with a G on the template strand</b>
This molecule has 111 solvent sites and 16 intermolecular hydrogen bonds.
<br>-What base is the incoming nucleotide? <b>C</b>
<br>-How does the incoming nucleotide differ from the last nucleotide of the primer? <b>The incoming nucleotide still has 3 phosphate groups, whereas the incorporated nucleotide only has one phosphate group.</b>
<br>-One ion is near the site of chemistry. What is it? <b>Mg<sup>2+</sup></b>
<br>-Would you expect this to be significant for catalysis? <b> Yes. It promotes deprotonation of the 3' OH of the primer strand and assists that leaving of the pyrophosphate. </b>


===<br><b>Page 4: SCHEMATIC INTERACTIONS OF TWO CHAINS</b>===
===Ligand===


<br>-Look at the nucleotide of the template that is 5' of the one base-pared to the last nucleotide ofthe primer. Could the first nucleotide of the template potentially base-pair to the incoming nucleotide? <b> Yes</b>
Ion copper in the oxidized state 2 + is localized at one end of the molecule, 6 Å below the surface. The copper atom is in the core of a hydrophobic patch composed of residues His-37, Cys-84, His-87 and Met-92.  This copper binding site has a distorted trigonal pyramidal shape. The base of the pyramide is composed of one sulfur from a cysteine and two nitrogen atoms from two different histidins and the apex is formed by one sulfur from a methionin. The distortion occurs on the bond between the copper and the sulfur atom.
<br>- Are they base-paired in the structure? <b> Yes</b>
Plastocyanin in the reduced form with ion copper in the form +1 has a different copper binding site shape. His-87 a residue of the hydrophobic patch will be protonated and the copper site has a trigonal planar structure.
<br>-Is the incoming base paired to any nucleic acid? <b> No </b>
<br>-What type of regular secondary structure element dominates in the protein? <b>Alpha-helices</b>
<br> -What do you need to make an abundant amount of double stranded product of a particular size using this enzyme? <b> PCR Machine, dNTP's, primers, template. </b>


==<b>Part II</b>==  
=='''Role in Photosynthesis'''==
===<b> Page 5:</b>===
===Context===
<br>-Does the new structure include essentially the same protein as in the original structure? <b> Yes</b>
<br>-What is the pbd identification code of the new structure? <b>3KTQ</b>
<br>-What is the resolution of this new structure? <b>2.3 Angstrom</b>
<br> -Which chain is the template in the new structure? <b> Chain C</b>
<br>-What is the distance between the oxygen atom of the sidechain of residue 671 in Chain A and the oxygen atom of the base of the incoming nucleotide in 3ktq? <b></b>


===<b>Page 6:</b>===
In the sunlight reaction, in photosynthesis, plastocyanin is an important electron donor to the Photosystem I (P700).Thanks to its hydrophobic surface, plastocyanin is localised in the intern membrane of the thylakoid in chloroplasts. Its redox potential, about 370 mV, has allowed to determine the place of plastocyanin in the electron transport chain (between the photosystem II and the photosystem I): between the cytochrome b<sub>6</sub>f complex and the photosystem I.
<br>-In 2KTQ, what is the distance between the oxygen atom of the sidechain of residue 671 in Chain A and the oxygen atom of the base of the incoming nucleotide? <b>9.78 Angstrom</b>
Plastocyanin receive an electron from the cytochrome b<sub>6</sub>f complex and give up its electron to the photosystem I [http://www.springerlink.com/content/g5n15867765m52h4/ Journal of Bioenergetics and Biomembranes ].
<br> -Assuming the end of the primer and the incoming nucleotide sit in essentially that same place in the active site of both 2KTQ and 3KTQ, has 671 undergone a substantial shift between the two structures?
 
<br> -In 3KTQ, look at the nucleotide of the template that is 5' of the one base-paired to the last nucleotide of the primer. Could this nucleotide of the template potentially base-pair to the incoming nucleotide?
===Electron Transfer Mechanism===
<br> -Are they base-paired in 3KTQ?
 
<applet load='1d66' size='300' frame='true' align='right' scene='Sandbox_142/Distance_oxygen_oxygen3ktq/2' caption='3ktq' />
The copper atom bound to the plastocyanin is in the shape Cu<sup>2+</sup>. This  shape of plastocyanin is reduced by the cytochrome b<sub>6</sub>f according to the following reaction :
<applet load='1d66' size='300' frame='true' align='left' scene='Sandbox_142/Distance_oxygen_oxygen_2ktq/1' caption='2ktq' />
:Cu<sup>2+</sup>Pc + e<sup>-</sup> &rarr; Cu<sup>+</sup>Pc
The electron is given up by the cytochrome b<sub>6</sub>f and transforms plastocyanin in shape Cu<sup>2+</sup> into plastocyanin in shape Cu<sup>+</sup>.
Then this plastocyanin diffuses through the lumen of thylakoid (remember its localisation in intern membrane of the thylakoid) until the recognition/binding occurs with the photosystem I.
Photosystem I (P700) oxidizes Cu<sup>+</sup>Pc according to the following reaction :
:Cu<sup>+</sup>Pc &rarr; Cu<sup>2+</sup>Pc + e<sup>-</sup>
P700 become P700<sup>+</sup>. Photosystem I, now actived, can produces NADPH. This NADPH will be used in the dark reaction of photosynthesis.
 
=='''References'''==
:1.Coller, C.A., Guss, J.M., Sugimura, Y., and Yoshizaki, F. (1989) Crystal Structure of Plastocyanin from a Green Alga, Enteromorpha prolifera, J. Mol. Biol. (1990) '''211''', 617-632.[[http://www.sciencedirect.com/science/article/pii/002228369090269R]]
:2.Colman, P.M., Freeman, H.C., Guss, J.M., Murata, M., Norris, V.A., Ramshaw, J.A.M. and Venkatappa M.P.(1978)Nature (Lond.) '''272''', 319-324. [[http://www.nature.com/nature/journal/v272/n5651/abs/272319a0.html]]
:3.Simpson J. R., Moritz, L.R., Nice, E.C., Grego, B. and Yoshizak, F. (1986)Complete amino acid sequence of plastocyanin from  a green alga, Enteromorpha prolifera, Eur.J. Biochem. '''157''', 497-506. [[http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1986.tb09694.x/pdf]]
:4.Cookson, D. J., Hayes, M. T. and Wright, P. E. (1980) Nature (Lond.) '''283''', 682-683. [[http://www.springerlink.com/content/g5n15867765m52h4/]]
:5.Handford, P. M., Hill, H. A. O., Lee, R. W.-K., Henderson, R.A. and Sykes, A. G. (1980) J. Inorg. Biochem. '''13''', 83-88.[[http://www.springerlink.com/content/v429428w64w5vv5v/]]
:6.Chothia and Lesk, 1982; Guss and Freeman, 1983.
 
=='''Proteopedia Page Contributors and Editors'''==
 
Mathilde BICHELBERGER and Morgane RAPHALEN

Latest revision as of 14:31, 31 December 2011

Plastocyanin from a Green Alga, Enteromorpha prolifera

Please do NOT make changes to this sandbox. This sandbox is currently reserved, ESBS for use of Protopedia project. Bichelberger and Raphalen.

Protein name : plastocyanin; Organism : Enteromorpha prolifera; Taxonomie : Eukaryota › Viridiplantae › Chlorophyta › Ulvophyceae › Ulvales › Ulvaceae › Ulva; Resolution : 1.80 Å; Poids : 10,500 D

Drag the structure with the mouse to rotate


OverviewOverview

Plastocyanin is an important copper-containing protein involved in photosynthesis by all higher plants and some algae namely by Enteromorpha prolifera. Plastocyanin extracted from this alga, was the first algal blue copper protein characterized by X-ray crystallography and one of the best characterized electron transfer protein of the photosynthetic apparatus. This protein was intensively studied between 1981 and 1994 because of these particular spectroscopic and electronic properties. The high resolution structural analysis by molecular replacement in 1989 provided an accurate description of the structure of this protein. J. Mol. Biol. Plastocyanin is an electron donor localized in the intern membrane of thylakoïd in chloroplast. This is a monomeric protein with a single polypeptide chain of 98 amino acids and one copper atom. The molecular weight of plastocyanin is around 10,500 Daltons.

StructureStructure

Residue distributionResidue distribution

Plastocyanin extracted from a Green Alga, Enteromorpha prolifera, has a β-sandwich structure as a slightly flattened cylinder with approximate dimensions 40 Å × 32 Å × 28 Å. Nature This β-sandwich is composed of two β-sheets (I and II) separated by a hydrophobic core. Turns on the two β-sheets occur between residues 42 to 45 and 47 to 50. Seven strands (1 to 4 and 6 to 8) of the polypeptide backbone have substantial β character and contribute to the β-sheets. The 5 strand has no β character and formed a helical segment. The symmetry of this molecule related on an van der Waals’ bond on the northern loop between strands 3 and 4 the side-chain of Pro36 which contacts Gln 68. This plastocyanin includes important “acidic patch” which is localized between residues 59 to 61 and 42 to 45. Eur.J. Biochem. This acidic patch is significant in electron transfer namely facilitating electrostatic recognition of her redox partner( see Role in Photosynthesis). This molecule has 111 solvent sites and 16 intermolecular hydrogen bonds.

LigandLigand

Ion copper in the oxidized state 2 + is localized at one end of the molecule, 6 Å below the surface. The copper atom is in the core of a hydrophobic patch composed of residues His-37, Cys-84, His-87 and Met-92. This copper binding site has a distorted trigonal pyramidal shape. The base of the pyramide is composed of one sulfur from a cysteine and two nitrogen atoms from two different histidins and the apex is formed by one sulfur from a methionin. The distortion occurs on the bond between the copper and the sulfur atom. Plastocyanin in the reduced form with ion copper in the form +1 has a different copper binding site shape. His-87 a residue of the hydrophobic patch will be protonated and the copper site has a trigonal planar structure.

Role in PhotosynthesisRole in Photosynthesis

ContextContext

In the sunlight reaction, in photosynthesis, plastocyanin is an important electron donor to the Photosystem I (P700).Thanks to its hydrophobic surface, plastocyanin is localised in the intern membrane of the thylakoid in chloroplasts. Its redox potential, about 370 mV, has allowed to determine the place of plastocyanin in the electron transport chain (between the photosystem II and the photosystem I): between the cytochrome b6f complex and the photosystem I. Plastocyanin receive an electron from the cytochrome b6f complex and give up its electron to the photosystem I Journal of Bioenergetics and Biomembranes .

Electron Transfer MechanismElectron Transfer Mechanism

The copper atom bound to the plastocyanin is in the shape Cu2+. This shape of plastocyanin is reduced by the cytochrome b6f according to the following reaction :

Cu2+Pc + e- → Cu+Pc

The electron is given up by the cytochrome b6f and transforms plastocyanin in shape Cu2+ into plastocyanin in shape Cu+. Then this plastocyanin diffuses through the lumen of thylakoid (remember its localisation in intern membrane of the thylakoid) until the recognition/binding occurs with the photosystem I. Photosystem I (P700) oxidizes Cu+Pc according to the following reaction :

Cu+Pc → Cu2+Pc + e-

P700 become P700+. Photosystem I, now actived, can produces NADPH. This NADPH will be used in the dark reaction of photosynthesis.

ReferencesReferences

1.Coller, C.A., Guss, J.M., Sugimura, Y., and Yoshizaki, F. (1989) Crystal Structure of Plastocyanin from a Green Alga, Enteromorpha prolifera, J. Mol. Biol. (1990) 211, 617-632.[[1]]
2.Colman, P.M., Freeman, H.C., Guss, J.M., Murata, M., Norris, V.A., Ramshaw, J.A.M. and Venkatappa M.P.(1978)Nature (Lond.) 272, 319-324. [[2]]
3.Simpson J. R., Moritz, L.R., Nice, E.C., Grego, B. and Yoshizak, F. (1986)Complete amino acid sequence of plastocyanin from a green alga, Enteromorpha prolifera, Eur.J. Biochem. 157, 497-506. [[3]]
4.Cookson, D. J., Hayes, M. T. and Wright, P. E. (1980) Nature (Lond.) 283, 682-683. [[4]]
5.Handford, P. M., Hill, H. A. O., Lee, R. W.-K., Henderson, R.A. and Sykes, A. G. (1980) J. Inorg. Biochem. 13, 83-88.[[5]]
6.Chothia and Lesk, 1982; Guss and Freeman, 1983.

Proteopedia Page Contributors and EditorsProteopedia Page Contributors and Editors

Mathilde BICHELBERGER and Morgane RAPHALEN

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Student, Mathilde Bichelberger
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