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PDBsum entry 1v2b
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protein ligands Protein-protein interface(s) links
Photosynthesis PDB id
1v2b

 

 

 

 

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Contents
Protein chains
148 a.a. *
151 a.a. *
Ligands
GLC ×2
SO4 ×2
Waters ×433
* Residue conservation analysis
PDB id:
1v2b
Name: Photosynthesis
Title: Crystal structure of psbp protein in the oxygen-evolving complex of photosystem ii from higher plants
Structure: 23-kda polypeptide of photosystem ii oxygen-evolving complex. Chain: a, b. Fragment: residues 10-186. Synonym: oxygen-evolving complex 23-kda protein. Engineered: yes
Source: Nicotiana tabacum. Common tobacco. Organism_taxid: 4097. Gene: psbp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.60Å     R-factor:   0.187     R-free:   0.207
Authors: K.Ifuku,T.Nakatsu,H.Kato,F.Sato,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
K.Ifuku et al. (2004). Crystal structure of the PsbP protein of photosystem II from Nicotiana tabacum. EMBO Rep, 5, 362-367. PubMed id: 15031714 DOI: 10.1038/sj.embor.7400113
Date:
14-Oct-03     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18212  (PSBP2_TOBAC) -  Oxygen-evolving enhancer protein 2-2, chloroplastic from Nicotiana tabacum
Seq:
Struc: 		265 a.a.
148 a.a.*
Protein chain
Pfam   ArchSchema ?
P18212  (PSBP2_TOBAC) -  Oxygen-evolving enhancer protein 2-2, chloroplastic from Nicotiana tabacum
Seq:
Struc: 		265 a.a.
151 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 

 
DOI no: 10.1038/sj.embor.7400113 EMBO Rep 5:362-367 (2004)
PubMed id: 15031714  
 
 
Crystal structure of the PsbP protein of photosystem II from Nicotiana tabacum.
K.Ifuku, T.Nakatsu, H.Kato, F.Sato.
 
  ABSTRACT  
 
PsbP is a membrane-extrinsic subunit of the water-oxidizing complex photosystem II (PS II). The evolutionary origin of PsbP has long been a mystery because it specifically exists in higher plants and green algae but not in cyanobacteria. We report here the crystal structure of PsbP from Nicotiana tabacum at a resolution of 1.6 A. Its structure is mainly composed of beta-sheet, and is not similar to any structures in cyanobacterial PS II. However, the electrostatic surface potential of PsbP is similar to that of cyanobacterial PsbV (cyt c(550)), which has a function similar to PsbP. A structural homology search with the DALI algorithm indicated that the folding of PsbP is very similar to that of Mog1p, a regulatory protein for the nuclear transport of Ran GTPase. The structure of PsbP provides insight into its novel function in GTP-regulated metabolism in PS II.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Stereo view of the structure of PsbP. The schematic representation of the PsbP structural model shows a series of -strands that are derived from residues 16 -53 (domain I: pink) and the central six-stranded antiparallel -sheet flanked on both sides by helices (domain II: blue). The N (residue 16) and C (residue 186) termini are labelled. The position of the Asn 58 -Val 59 bond is indicated by an arrow. The figure was generated with PyMOL (http://www.pymol.org). 		Figure 3.
Figure 3 Comparison of the electrostatic surface potentials of (A) PsbP from N. tabacum (this study) and (B) PsbV from Thermosynechococcus elongatus (Kerfeld et al, 2003). The molecules are rotated anticlockwise by 90° and 180° around a vertical axis (left to right). The figure was produced using GRASP (Nicholls et al, 1991).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO Rep (2004, 5, 362-367) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21487931 C.Pagliano, F.Chimirri, G.Saracco, F.Marsano, and J.Barber (2011).
One-step isolation and biochemical characterization of a highly active plant PSII monomeric core.
  Photosynth Res, 108, 33-46.  
20352642 A.Guskov, A.Gabdulkhakov, M.Broser, C.Glöckner, J.Hellmich, J.Kern, J.Frank, F.Müh, W.Saenger, and A.Zouni (2010).
Recent progress in the crystallographic studies of photosystem II.
  Chemphyschem, 11, 1160-1171.  
20666928 K.Ifuku, S.Ishihara, and F.Sato (2010).
Molecular functions of oxygen-evolving complex family proteins in photosynthetic electron flow.
  J Integr Plant Biol, 52, 723-734.  
19944772 N.Sato (2010).
Phylogenomic and structural modeling analyses of the PsbP superfamily reveal multiple small segment additions in the evolution of photosystem II-associated PsbP protein in green plants.
  Mol Phylogenet Evol, 56, 176-186.  
20375107 R.Nagao, T.Suzuki, A.Okumura, A.Niikura, M.Iwai, N.Dohmae, T.Tomo, J.R.Shen, M.Ikeuchi, and I.Enami (2010).
Topological analysis of the extrinsic PsbO, PsbP and PsbQ proteins in a green algal PSII complex by cross-linking with a water-soluble carbodiimide.
  Plant Cell Physiol, 51, 718-727.  
19033288 C.Pagliano, N.La Rocca, F.Andreucci, Z.Deák, I.Vass, N.Rascio, and R.Barbato (2009).
The extreme halophyte Salicornia veneta is depleted of the extrinsic PsbQ and PsbP proteins of the oxygen-evolving complex without loss of functional activity.
  Ann Bot (Lond), 103, 505-515.  
  19193998 J.Kohoutová, I.Kutá Smatanová, J.Brynda, M.Lapkouski, J.L.Revuelta, J.B.Arellano, and R.Ettrich (2009).
Crystallization and preliminary crystallographic characterization of the extrinsic PsbP protein of photosystem II from Spinacia oleracea.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 111-115.  
18780158 A.K.Williamson (2008).
Structural and functional aspects of the MSP (PsbO) and study of its differences in thermophilic versus mesophilic organisms.
  Photosynth Res, 98, 365-389.  
18709442 B.Lundin, M.Nurmi, M.Rojas-Stuetz, E.M.Aro, I.Adamska, and C.Spetea (2008).
Towards understanding the functional difference between the two PsbO isoforms in Arabidopsis thaliana-insights from phenotypic analyses of psbo knockout mutants.
  Photosynth Res, 98, 405-414.  
18791807 K.Ifuku, S.Ishihara, R.Shimamoto, K.Ido, and F.Sato (2008).
Structure, function, and evolution of the PsbP protein family in higher plants.
  Photosynth Res, 98, 427-437.  
18937045 Y.Yamamoto, R.Aminaka, M.Yoshioka, M.Khatoon, K.Komayama, D.Takenaka, A.Yamashita, N.Nijo, K.Inagawa, N.Morita, T.Sasaki, and Y.Yamamoto (2008).
Quality control of photosystem II: impact of light and heat stresses.
  Photosynth Res, 98, 589-608.  
17200881 J.L.Roose, K.M.Wegener, and H.B.Pakrasi (2007).
The extrinsic proteins of Photosystem II.
  Photosynth Res, 92, 369-387.  
16407186 C.Dabney-Smith, H.Mori, and K.Cline (2006).
Oligomers of Tha4 organize at the thylakoid Tat translocase during protein transport.
  J Biol Chem, 281, 5476-5483.  
16669773 N.Nelson, and C.F.Yocum (2006).
Structure and function of photosystems I and II.
  Annu Rev Plant Biol, 57, 521-565.  
16948158 Q.Xu, S.S.Krishna, D.McMullan, R.Schwarzenbacher, M.D.Miller, P.Abdubek, S.Agarwalla, E.Ambing, T.Astakhova, H.L.Axelrod, J.M.Canaves, D.Carlton, H.J.Chiu, T.Clayton, M.DiDonato, L.Duan, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, E.Koesema, A.Kreusch, P.Kuhn, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, K.Quijano, R.Reyes, C.L.Rife, G.Spraggon, R.C.Stevens, H.van den Bedem, A.White, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2006).
Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p.
  Proteins, 65, 777-782.
PDB code: 1vr8
16723351 Y.Kashino, N.Inoue-Kashino, J.L.Roose, and H.B.Pakrasi (2006).
Absence of the PsbQ protein results in destabilization of the PsbV protein and decreased oxygen evolution activity in cyanobacterial photosystem II.
  J Biol Chem, 281, 20834-20841.  
16049782 K.Ifuku, T.Nakatsu, R.Shimamoto, Y.Yamamoto, S.Ishihara, H.Kato, and F.Sato (2005).
Structure and function of the PsbP protein of photosystem II from higher plants.
  Photosynth Res, 84, 251-255.  
16049783 Y.Ishikawa, W.P.Schröder, and C.Funk (2005).
Functional analysis of the PsbP-like protein (sll1418) in Synechocystis sp. PCC 6803.
  Photosynth Res, 84, 257-262.  
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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