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PDBsum entry 1iuz

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protein ligands metals links
Electron transport PDB id
1iuz
Jmol
Contents
Protein chain
98 a.a. *
Ligands
SO4
Metals
_CU
Waters ×105
* Residue conservation analysis
PDB id:
1iuz
Name: Electron transport
Title: Plastocyanin
Structure: Plastocyanin. Chain: a
Source: Ulva pertusa. Organism_taxid: 3120
Resolution:
1.60Å     R-factor:   0.176     R-free:   0.211
Authors: N.Shibata
Key ref:
N.Shibata et al. (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. PubMed id: 9933621 DOI: 10.1074/jbc.274.7.4225
Date:
06-Oct-96     Release date:   20-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56274  (PLAS_ULVPE) -  Plastocyanin
Seq:
Struc:
98 a.a.
98 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     electron carrier activity     3 terms  

 

 
DOI no: 10.1074/jbc.274.7.4225 J Biol Chem 274:4225-4230 (1999)
PubMed id: 9933621  
 
 
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.
N.Shibata, T.Inoue, C.Nagano, N.Nishio, T.Kohzuma, K.Onodera, F.Yoshizaki, Y.Sugimura, Y.Kai.
 
  ABSTRACT  
 
The crystal structure of plastocyanin from a green alga, Ulva pertusa, has been determined at 1.6-A resolution. At its copper site, U. pertusa plastocyanin has a distorted tetrahedral coordination geometry similar to other plastocyanins. In comparison with structures of plastocyanins reported formerly, a Cu(II)-Sdelta(Met92) bond distance (2.69 A) is shorter by about 0.2 A and a Cu(II)-Sgamma(Cys84) distance is longer by less than 0.1 A in U. pertusa plastocyanin. These subtle but significant differences are caused by the structural change at a His-Met loop (His87-Met92) due to an absence of a O(Asp85)-Ogamma(Ser88) hydrogen bond which is found in Enteromorpha prolifera plastocyanin. In addition, poplar and Chlamydomonas reinhardtii plastocyanins with a glutamine at residue 88 have a weak cation-pi interaction with Tyr83. This interaction lengthens the Cu(II)-Sdelta(Met92) bond of poplar and C. reinhardtii plastocyanins by 0.14 and 0.20 A, respectively. As a result of structural differences, U. pertusa plastocyanin has a less distorted geometry than the other plastocyanins. Thus, the cupric geometry is finely tuned by the interactions between residues 85 and 88 and between residues 83 and 88. This result implies that the copper site is more flexible than reported formerly and that the rack mechanism would be preferable to the entatic theory. The His-Met loop may regulate the electron transfer rate within the complex between plastocyanin and cytochrome f.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Amino acid sequences of plastocyanin from U. pertusa,1 E. prolifera (52), C. reinhardtii (53), S. obliquus (7, 8), Chlorella fusca (54), A. variabilis (55), Synechocystis PCC6803 (56), Silene latifolia (57), Arabidopsis thaliana (58), Spinacia oleracea (59), Populus nigra a (3), Pisum sativum (60), Nicotiana tabacum a (61), Lycopersicon esculentum (62), Phaseolus vulgaris (63), Cucurbita pepo (64), Petroselinum crispum (65), and Prochlorothrix hollandica (66).
Figure 4.
Fig. 4. Ball-and-stick models at the copper site with a 2F[o] F[c] electron density map. The map was contoured at a level of 1.5 .
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 4225-4230) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21258692 M.Choi, and V.L.Davidson (2011).
Cupredoxins--a study of how proteins may evolve to use metals for bioenergetic processes.
  Metallomics, 3, 140-151.  
19572723 N.P.Mankad, S.B.Harkins, W.E.Antholine, and J.C.Peters (2009).
Multifrequency EPR studies of [Cu(1.5)Cu(1.5)](+) for Cu2(mu-NR2)2 and Cu2(mu-PR2)2 diamond cores.
  Inorg Chem, 48, 7026-7032.  
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.  
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.  
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
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.  
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.