spacer
spacer

PDBsum entry 1pcs
Go to PDB code: 
protein metals links
Electron transport PDB id
1pcs

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
98 a.a. *
Metals
_CU
Waters ×225
* Residue conservation analysis
PDB id:
1pcs
Name: Electron transport
Title: The 2.15 a crystal structure of a triple mutant plastocyanin from the cyanobacterium synechocystis sp. Pcc 6803
Structure: Plastocyanin. Chain: a. Engineered: yes. Mutation: yes
Source: Synechocystis sp.. Organism_taxid: 1148. Strain: pcc 6803. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.15Å     R-factor:   0.167     R-free:   0.220
Authors: A.Romero,B.De La Cerda,P.F.Varela,J.A.Navarro,M.Hervas,M.A.De La Rosa
Key ref:
A.Romero et al. (1998). The 2.15 A crystal structure of a triple mutant plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803. J Mol Biol, 275, 327-336. PubMed id: 9466912 DOI: 10.1006/jmbi.1997.1455
Date:
17-Jun-97     Release date:   17-Dec-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21697  (PLAS_SYNY3) -  Plastocyanin from Synechocystis sp. (strain PCC 6803 / Kazusa)
Seq:
Struc: 		126 a.a.
98 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1006/jmbi.1997.1455 J Mol Biol 275:327-336 (1998)
PubMed id: 9466912  
 
 
The 2.15 A crystal structure of a triple mutant plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803.
A.Romero, B.De la Cerda, P.F.Varela, J.A.Navarro, M.Hervás, M.A.De la Rosa.
 
  ABSTRACT  
 
The crystal structure of the triple mutant A42D/D47P/A63L plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803 has been determined by Patterson search methods using the known structure of the poplar protein. Crystals of the triple mutant A42D/D47P/A63L, which are stable for days in its oxidized form, were grown from ammonium sulfate, with the cell constants a = b = 34.3 A and c = 111.8 A belonging to space group P3(2)21. The structure was refined using restrained crystallographic refinement to an R-factor of 16.7% for 4070 independent reflections between 8.0 and 2.15 A with intensities greater than 2 sigma (I), with root mean square deviations of 0.013 A and 1.63 degrees from ideal bond lengths and bond angles, respectively. The final model comprises 727 non-hydrogen protein atoms within 98 residues, 75 water molecules and a single copper ion. The overall tertiary fold of Synechocystis plastocyanin consists of a compact ellipsoidal beta-sandwich structure made up of two beta-sheets embracing a hydrophobic core. Each sheet contains parallel and antiparallel beta-strands. In addition to the beta-sheets, the structure contains an alpha-helix from Pro47 to Lys54 that follows beta-strand 4. The three-dimensional structure of Synechocystis plastocyanin is thus similar to those reported for the copper protein isolated from eukaryotic organisms and, in particular, from the cyanobacterium Anabaena variabilis, the only cyanobacterial plastocyanin structure available so far. The molecule holds an hydrophobic region surrounding His87, as do other plastocyanins, but the lack of negatively charged residues at the putative distant remote site surrounding Tyr83 could explain why the Synechocystis protein exhibits a collisional reaction mechanism for electron transfer to photosystem I (PSI), which involves no formation of the transient plastocyanin-PSI complex kinetically observed in green algae and higher plants.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo diagram of the final 2 F[o] − F[c] map, contoured at 1.0 σ, showing the copper binding site of Synechocystis mutant plastocyanin. The copper site primarily has N2S2 coordination and is ligated in a T1 distorted tetrahedral geometry by His37, His87, Cys84 and Met92. 		Figure 5.
Figure 5. Electrostatic potential mapping at the molecular surface of plastocyanin from Synechocystis, poplar , C. reinhardtii and E. prolifera as viewed in the relatively same orientation. The protein molecule is depicted by a solid surface, colored according to the calculated electrostatic potential and contoured from −8 (intense red) to +8kT/e (intense blue). The Figure was made with GRASP (Nicholls et al., 1993).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 275, 327-336) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21276936 J.Chaboy, S.Díaz-Moreno, I.Díaz-Moreno, M.A.De la Rosa, and A.Díaz-Quintana (2011).
How the local geometry of the Cu-binding site determines the thermal stability of blue copper proteins.
  Chem Biol, 18, 25-31.  
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
15291822 J.A.Navarro, C.E.Lowe, R.Amons, T.Kohzuma, G.W.Canters, M.A.De la Rosa, M.Ubbink, and M.Hervás (2004).
Functional characterization of the evolutionarily divergent fern plastocyanin.
  Eur J Biochem, 271, 3449-3456.  
14672950 M.Paumann, B.Lubura, G.Regelsberger, M.Feichtinger, G.Köllensberger, C.Jakopitsch, P.G.Furtmüller, G.A.Peschek, and C.Obinger (2004).
Soluble CuA domain of cyanobacterial cytochrome c oxidase.
  J Biol Chem, 279, 10293-10303.  
14517909 D.Monleón, and B.Celda (2003).
Study of electrostatic potential surface distribution of wild-type plastocyanin Synechocystis solution structure determined by homonuclear NMR.
  Biopolymers, 70, 212-220.
PDB code: 1m9w
11988476 M.Ubbink, J.A.Worrall, G.W.Canters, E.J.Groenen, and M.Huber (2002).
Paramagnetic resonance of biological metal centers.
  Annu Rev Biophys Biomol Struct, 31, 393-422.  
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
  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.  
10224089 B.De la Cerda, A.Díaz-Quintana, J.A.Navarro, M.Hervás, and M.A.De la Rosa (1999).
Site-directed mutagenesis of cytochrome c6 from Synechocystis sp. PCC 6803. The heme protein possesses a negatively charged area that may be isofunctional with the acidic patch of plastocyanin.
  J Biol Chem, 274, 13292-13297.  
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
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
  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
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.

 

spacer
spacer