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protein metals links
Electron transport PDB id
1ag6
Jmol
Contents
Protein chain
99 a.a. *
Metals
_CU
Waters ×64
* Residue conservation analysis
PDB id:
1ag6
Name: Electron transport
Title: Plastocyanin from spinach
Structure: Plastocyanin. Chain: a. Engineered: yes. Mutation: yes
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Cell_line: bl21. Cellular_location: thylakoid. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.60Å     R-factor:   0.191     R-free:   0.224
Authors: Y.Xue,M.Okvist,S.Young
Key ref:
Y.Xue et al. (1998). Crystal structure of spinach plastocyanin at 1.7 A resolution. Protein Sci, 7, 2099-2105. PubMed id: 9792096 Ref: Full text
Date:
02-Apr-97     Release date:   21-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00289  (PLAS_SPIOL) -  Plastocyanin, chloroplastic
Seq:
Struc: 		168 a.a.
99 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     electron carrier activity     2 terms  

 

 
Full text Protein Sci 7:2099-2105 (1998)
PubMed id: 9792096  
 
 
Crystal structure of spinach plastocyanin at 1.7 A resolution.
Y.Xue, M.Okvist, O.Hansson, S.Young.
 
  ABSTRACT  
 
The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins.
 
  Selected figure(s)  
 
Figure 1.
ig. 1. Electron density map (ZF, - Fc), contoured at 1.5a, showing well-defined holes the phenyl rings f Phel4, phe29, and Plot produced with O/oplot (Jones t al., 1991). 		Figure 2.
Fig. 2. Superposition of GlySAsp spinach PC (thick lines) and poplar PC (thin lines). A: C, traces. B: Illustration of similarities in intramolecular contacts, and the differences in intermolecular contacts, for Asp8 in the mutant spinach PC and poplar PC. Plots produced with Setor(Evans, 1993).
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 2099-2105) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18250895 C.Dennison (2008).
The role of ligand-containing loops at copper sites in proteins.
  Nat Prod Rep, 25, 15-24.  
18433287 D.N.LeBard, and D.V.Matyushov (2008).
Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation.
  J Chem Phys, 128, 155106.  
19256862 D.N.Lebard, and D.V.Matyushov (2008).
Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins.
  Phys Rev E Stat Nonlin Soft Matter Phys, 78, 061901.  
18830805 R.Razeghifard (2008).
Artificial photoactive proteins.
  Photosynth Res, 98, 677-685.  
17972160 E.L.Gross (2007).
A Brownian Dynamics computational study of the interaction of spinach plastocyanin with turnip cytochrome f: the importance of plastocyanin conformational changes.
  Photosynth Res, 94, 411-422.  
16446449 D.F.Hansen, and J.J.Led (2006).
Determination of the geometric structure of the metal site in a blue copper protein by paramagnetic NMR.
  Proc Natl Acad Sci U S A, 103, 1738-1743.  
16432723 D.Flemming Hansen, S.I.Gorelsky, R.Sarangi, K.O.Hodgson, B.Hedman, H.E.Christensen, E.I.Solomon, and J.J.Led (2006).
Reinvestigation of the method used to map the electronic structure of blue copper proteins by NMR relaxation.
  J Biol Inorg Chem, 11, 277-285.  
16570184 K.N.Sas, A.Haldrup, L.Hemmingsen, E.Danielsen, and L.H.Øgendal (2006).
pH-dependent structural change of reduced spinach plastocyanin studied by perturbed angular correlation of gamma-rays and dynamic light scattering.
  J Biol Inorg Chem, 11, 409-418.  
16795108 K.Sato, and C.Dennison (2006).
Active site comparison of CoII blue and green nitrite reductases.
  Chemistry, 12, 6647-6659.  
16504567 T.M.Iverson (2006).
Evolution and unique bioenergetic mechanisms in oxygenic photosynthesis.
  Curr Opin Chem Biol, 10, 91.  
16981015 W.R.Hagen (2006).
EPR spectroscopy as a probe of metal centres in biological systems.
  Dalton Trans, 0, 4415-4434.  
16234922 C.Dennison (2005).
Ligand and loop variations at type 1 copper sites: influence on structure and reactivity.
  Dalton Trans, 0, 3436-3442.  
15750998 G.Battistuzzi, M.Borsari, G.Di Rocco, A.Leonardi, A.Ranieri, and M.Sola (2005).
Electrostatic effects on the thermodynamics of protonation of reduced plastocyanin.
  Chembiochem, 6, 692-696.  
15573135 N.Nelson, and A.Ben-Shem (2004).
The complex architecture of oxygenic photosynthesis.
  Nat Rev Mol Cell Biol, 5, 971-982.  
14668855 A.Ben-Shem, F.Frolow, and N.Nelson (2003).
Crystal structure of plant photosystem I.
  Nature, 426, 630-635.
PDB code: 1qzv
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
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.  
11714931 A.Bergkvist, M.Ejdebäck, M.Ubbink, and B.G.Karlsson (2001).
Surface interactions in the complex between cytochrome f and the E43Q/D44N and E59K/E60Q plastocyanin double mutants as determined by (1)H-NMR chemical shift analysis.
  Protein Sci, 10, 2623-2626.  
11720977 F.De Rienzo, R.R.Gabdoulline, M.C.Menziani, P.G.De Benedetti, and R.C.Wade (2001).
Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f.
  Biophys J, 81, 3090-3104.  
11371205 G.Battistuzzi, M.Borsari, L.Loschi, M.C.Menziani, F.De Rienzo, and M.Sola (2001).
Control of metalloprotein reduction potential: the role of electrostatic and solvation effects probed on plastocyanin mutants.
  Biochemistry, 40, 6422-6430.  
11369223 M.R.Jones, and P.K.Fyfe (2001).
Photosynthesis: new light on biological oxygen production.
  Curr Biol, 11, R318-R321.  
10611452 A.B.Hope (2000).
Electron transfers amongst cytochrome f, plastocyanin and photosystem I: kinetics and mechanisms.
  Biochim Biophys Acta, 1456, 5.  
  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.  
10819966 M.Ejdebäck, A.Bergkvist, B.G.Karlsson, and M.Ubbink (2000).
Side-chain interactions in the plastocyanin-cytochrome f complex.
  Biochemistry, 39, 5022-5027.  
10642183 M.J.Colaneri, J.Vitali, and J.Peisach (2000).
Electron spin-echo envelope modulation study of multicrystalline Cu(2+)-insulin: effects of Cd(2+) on the nuclear quadrupole interaction of the Cu(2+)-coordinated imidazole remote nitrogen.
  Biochemistry, 39, 584-591.  
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
10600133 K.Olesen, M.Ejdebäck, M.M.Crnogorac, N.M.Kostić, and O.Hansson (1999).
Electron transfer to photosystem 1 from spinach plastocyanin mutated in the small acidic patch: ionic strength dependence of kinetics and comparison of mechanistic models.
  Biochemistry, 38, 16695-16705.  
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.