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PDBsum entry 2plt
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protein metals links
Electron transport PDB id
2plt

 

 

 

 

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Contents
Protein chain
98 a.a. *
Metals
_CA
_CU
Waters ×79
* Residue conservation analysis
PDB id:
2plt
Name: Electron transport
Title: Structure determination of plastocyanin from a crystal specimen with hemihedral twinning fraction of one-half
Structure: Plastocyanin. Chain: a. Engineered: yes
Source: Chlamydomonas reinhardtii. Organism_taxid: 3055
Resolution:
1.50Å     R-factor:   0.168    
Authors: M.R.Redinbo,S.Merchant,T.O.Yeates
Key ref:
M.R.Redinbo et al. (1993). The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii. Biochemistry, 32, 10560-10567. PubMed id: 8399201 DOI: 10.1021/bi00091a005
Date:
06-May-93     Release date:   31-Oct-93    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18068  (PLAS_CHLRE) -  Plastocyanin, chloroplastic from Chlamydomonas reinhardtii
Seq:
Struc: 		145 a.a.
98 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi00091a005 Biochemistry 32:10560-10567 (1993)
PubMed id: 8399201  
 
 
The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii.
M.R.Redinbo, D.Cascio, M.K.Choukair, D.Rice, S.Merchant, T.O.Yeates.
 
  ABSTRACT  
 
The crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii has been determined at 1.5-A resolution with a crystallographic R factor of 16.8%. Plastocyanin is a small (98 amino acids), blue copper-binding protein that catalyzes the transfer of electrons in oxygenic photosynthesis from cytochrome f in the quinol oxidase complex to P700+ in photosystem I. Chlamydomonas reinhardtii plastocyanin is an eight-stranded, antiparallel beta-barrel with a single copper atom coordinated in quasitetrahedral geometry by two imidazole nitrogens (from His-37 and His-87), a cysteine sulfur (from Cys-84), and a methionine sulfur (from Met-92). The molecule contains a region of negative charge surrounding Tyr-83 (the putative distant site of electron transfer) and an exclusively hydrophobic region surrounding His-87; these regions are thought to be involved in the recognition of reaction partners for the purpose of directing electron transfer. Chlamydomonas reinhardtii plastocyanin is similar to the other plastocyanins of known structure, particularly the green algal plastocyanins from Enteromorpha prolifera and Scenedesmus obliquus. A potential "through-bond" path of electron transfer has been identified in the protein that involves the side chain of Tyr-83, the main-chain atoms between residues 83 and 84, the side chain of Cys-84, the copper atom, and the side chain of His-87.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20057046 V.Borshchevskiy, R.Efremov, E.Moiseeva, G.Büldt, and V.Gordeliy (2010).
Overcoming merohedral twinning in crystals of bacteriorhodopsin grown in lipidic mesophase.
  Acta Crystallogr D Biol Crystallogr, 66, 26-32.  
19177362 H.Fazelinia, P.C.Cirino, and C.D.Maranas (2009).
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.
  Protein Sci, 18, 180-195.  
16239335 E.J.Haddadian, and E.L.Gross (2006).
A Brownian dynamics study of the effects of cytochrome f structure and deletion of its small domain in interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii.
  Biophys J, 90, 566-577.  
16844750 E.J.Haddadian, and E.L.Gross (2006).
A Brownian dynamics study of the interactions of the luminal domains of the cytochrome b6f complex with plastocyanin and cytochrome c6: the effects of the Rieske FeS protein on the interactions.
  Biophys J, 91, 2589-2600.  
16214856 E.L.Gross, and I.Rosenberg (2006).
A Brownian dynamics study of the interaction of Phormidium cytochrome f with various cyanobacterial plastocyanins.
  Biophys J, 90, 366-380.  
16984911 F.Sommer, F.Drepper, W.Haehnel, and M.Hippler (2006).
Identification of precise electrostatic recognition sites between cytochrome c6 and the photosystem I subunit PsaF using mass spectrometry.
  J Biol Chem, 281, 35097-35103.  
16929103 L.Schmidt, H.E.Christensen, and P.Harris (2006).
Structure of plastocyanin from the cyanobacterium Anabaena variabilis.
  Acta Crystallogr D Biol Crystallogr, 62, 1022-1029.
PDB code: 2gim
16807973 S.Sinnecker, and F.Neese (2006).
QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study.
  J Comput Chem, 27, 1463-1475.  
15626695 E.J.Haddadian, and E.L.Gross (2005).
Brownian dynamics study of cytochrome f interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii plastocyanin, and cytochrome c6 mutants.
  Biophys J, 88, 2323-2339.  
15920618 V.Adaikkalam, and S.Swarup (2005).
Characterization of copABCD operon from a copper-sensitive Pseudomonas putida strain.
  Can J Microbiol, 51, 209-216.  
15345580 E.L.Gross (2004).
A Brownian dynamics study of the interaction of Phormidium laminosum plastocyanin with Phormidium laminosum cytochrome f.
  Biophys J, 87, 2043-2059.  
12944318 E.L.Gross, and D.C.Pearson (2003).
Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6.
  Biophys J, 85, 2055-2068.  
12207018 G.M.Soriano, L.W.Guo, C.De Vitry, T.Kallas, and W.A.Cramer (2002).
Electron transfer from the Rieske iron-sulfur protein (ISP) to cytochrome f in vitro. Is a guided trajectory of the ISP necessary for competent docking?
  J Biol Chem, 277, 41865-41871.  
11509552 I.Bertini, D.A.Bryant, S.Ciurli, A.Dikiy, C.O.Fernández, C.Luchinat, N.Safarov, A.J.Vila, and J.Zhao (2001).
Backbone dynamics of plastocyanin in both oxidation states. Solution structure of the reduced form and comparison with the oxidized state.
  J Biol Chem, 276, 47217-47226.
PDB codes: 1jxd 1jxf
11170377 Y.H.Pan, T.M.Epstein, M.K.Jain, and B.J.Bahnson (2001).
Five coplanar anion binding sites on one face of phospholipase A2: relationship to interface binding.
  Biochemistry, 40, 609-617.
PDB codes: 1fx9 1fxf
  10975566 F.De Rienzo, R.R.Gabdoulline, M.C.Menziani, and R.C.Wade (2000).
Blue copper proteins: a comparative analysis of their molecular interaction properties.
  Protein Sci, 9, 1439-1454.  
11092924 S.Yamada, S.Y.Park, H.Shimizu, Y.Koshizuka, K.Kadokura, T.Satoh, K.Suruga, M.Ogawa, Y.Isogai, T.Nishio, Y.Shiro, and T.Oku (2000).
Structure of cytochrome c6 from the red alga Porphyra yezoensis at 1. 57 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 1577-1582.
PDB code: 1gdv
10869174 Y.I.Chi, L.S.Huang, Z.Zhang, J.G.Fernández-Velasco, and E.A.Berry (2000).
X-ray structure of a truncated form of cytochrome f from chlamydomonas reinhardtii.
  Biochemistry, 39, 7689-7701.
PDB code: 1cfm
10213601 C.R.Babu, B.F.Volkman, and G.S.Bullerjahn (1999).
NMR solution structure of plastocyanin from the photosynthetic prokaryote, Prochlorothrix hollandica.
  Biochemistry, 38, 4988-4995.
PDB codes: 1b3i 2b3i
10089349 C.S.Bond, D.S.Bendall, H.C.Freeman, J.M.Guss, C.J.Howe, M.J.Wagner, and M.C.Wilce (1999).
The structure of plastocyanin from the cyanobacterium Phormidium laminosum.
  Acta Crystallogr D Biol Crystallogr, 55, 414-421.
PDB code: 1baw
9933621 N.Shibata, T.Inoue, C.Nagano, N.Nishio, T.Kohzuma, K.Onodera, F.Yoshizaki, Y.Sugimura, and Y.Kai (1999).
Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.
  J Biol Chem, 274, 4225-4230.
PDB code: 1iuz
10320332 T.Inoue, H.Sugawara, S.Hamanaka, H.Tsukui, E.Suzuki, T.Kohzuma, and Y.Kai (1999).
Crystal structure determinations of oxidized and reduced plastocyanin from the cyanobacterium Synechococcus sp. PCC 7942.
  Biochemistry, 38, 6063-6069.
PDB codes: 1bxu 1bxv
10206999 T.Kohzuma, T.Inoue, F.Yoshizaki, Y.Sasakawa, K.Onodera, S.Nagatomo, T.Kitagawa, S.Uzawa, Y.Isobe, Y.Sugimura, M.Gotowda, and Y.Kai (1999).
The structure and unusual pH dependence of plastocyanin from the fern Dryopteris crassirhizoma. The protonation of an active site histidine is hindered by pi-pi interactions.
  J Biol Chem, 274, 11817-11823.
PDB codes: 1kdi 1kdj
9790675 G.M.Soriano, M.V.Ponamarev, R.A.Piskorowski, and W.A.Cramer (1998).
Identification of the basic residues of cytochrome f responsible for electrostatic docking interactions with plastocyanin in vitro: relevance to the electron transfer reaction in vivo.
  Biochemistry, 37, 15120-15128.  
9784589 M.Hippler, K.Redding, and J.D.Rochaix (1998).
Chlamydomonas genetics, a tool for the study of bioenergetic pathways.
  Biochim Biophys Acta, 1367, 1.  
9551554 M.Ubbink, M.Ejdebäck, B.G.Karlsson, and D.S.Bendall (1998).
The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics.
  Structure, 6, 323-335.
PDB code: 2pcf
  9792096 Y.Xue, M.Okvist, O.Hansson, and S.Young (1998).
Crystal structure of spinach plastocyanin at 1.7 A resolution.
  Protein Sci, 7, 2099-2105.
PDB code: 1ag6
9341204 C.A.Libeu, M.Kukimoto, M.Nishiyama, S.Horinouchi, and E.T.Adman (1997).
Site-directed mutants of pseudoazurin: explanation of increased redox potentials from X-ray structures and from calculation of redox potential differences.
  Biochemistry, 36, 13160-13179.
PDB codes: 3paz 4paz 5paz 6paz 7paz 8paz
9281528 K.A.Koch, M.M.Peña, and D.J.Thiele (1997).
Copper-binding motifs in catalysis, transport, detoxification and signaling.
  Chem Biol, 4, 549-560.  
8756469 B.A.Brennan, J.G.Cummings, D.B.Chase, I.M.Turner, and M.J.Nelson (1996).
Resonance Raman spectroscopy of nitrile hydratase, a novel iron-sulfur enzyme.
  Biochemistry, 35, 10068-10077.  
8573585 F.Drepper, M.Hippler, W.Nitschke, and W.Haehnel (1996).
Binding dynamics and electron transfer between plastocyanin and photosystem I.
  Biochemistry, 35, 1282-1295.  
8931557 G.M.Soriano, M.V.Ponamarev, G.S.Tae, and W.A.Cramer (1996).
Effect of the interdomain basic region of cytochrome f on its redox reactions in vivo.
  Biochemistry, 35, 14590-14598.  
8679527 U.Badsberg, A.M.Jørgensen, H.Gesmar, J.J.Led, J.M.Hammerstad, L.L.Jespersen, and J.Ulstrup (1996).
Solution structure of reduced plastocyanin from the blue-green alga Anabaena variabilis.
  Biochemistry, 35, 7021-7031.
PDB code: 1nin
8591027 C.Frazão, C.M.Soares, M.A.Carrondo, E.Pohl, Z.Dauter, K.S.Wilson, M.Hervás, J.A.Navarro, M.A.De la Rosa, and G.M.Sheldrick (1995).
Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin.
  Structure, 3, 1159-1169.
PDB code: 1ctj
7559514 H.H.Li, and S.Merchant (1995).
Degradation of plastocyanin in copper-deficient Chlamydomonas reinhardtii. Evidence for a protease-susceptible conformation of the apoprotein and regulated proteolysis.
  J Biol Chem, 270, 23504-23510.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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