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PDBsum entry 2zt9

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protein ligands Protein-protein interface(s) links
Photosynthesis PDB id
2zt9
Jmol
Contents
Protein chains
215 a.a. *
160 a.a. *
289 a.a. *
166 a.a. *
31 a.a. *
32 a.a. *
37 a.a. *
29 a.a. *
Ligands
HEM ×4
UMQ ×3
CLA
OPC ×2
SQD
FES
BCR
Waters ×3
* Residue conservation analysis
PDB id:
2zt9
Name: Photosynthesis
Title: Crystal structure of the cytochrome b6f complex from nostoc 7120
Structure: Cytochrome b6. Chain: a. Cytochrome b6-f complex subunit 4. Chain: b. Synonym: 17 kda polypeptide. Apocytochrome f. Chain: c. Synonym: cytochrome f. Cytochrome b6-f complex iron-sulfur subunit 1.
Source: Nostoc sp. Pcc 7120. Organism_taxid: 103690. Organism_taxid: 103690
Resolution:
3.00Å     R-factor:   0.231     R-free:   0.259
Authors: W.A.Craner,Baniulis D.,Yamashita E.
Key ref:
D.Baniulis et al. (2009). Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120. J Biol Chem, 284, 9861-9869. PubMed id: 19189962 DOI: 10.1074/jbc.M809196200
Date:
27-Sep-08     Release date:   10-Feb-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A384  (CYB6_NOSS1) -  Cytochrome b6
Seq:
Struc:
215 a.a.
215 a.a.
Protein chain
Pfam   ArchSchema ?
Q93SX1  (PETD_NOSS1) -  Cytochrome b6-f complex subunit 4
Seq:
Struc:
160 a.a.
160 a.a.
Protein chain
Pfam   ArchSchema ?
Q93SW9  (CYF_NOSS1) -  Apocytochrome f
Seq:
Struc:
333 a.a.
289 a.a.
Protein chain
Pfam   ArchSchema ?
Q93SX0  (UCRIA_NOSS1) -  Cytochrome b6-f complex iron-sulfur subunit 1
Seq:
Struc:
179 a.a.
166 a.a.
Protein chain
Pfam   ArchSchema ?
Q8YVQ2  (PETL_NOSS1) -  Cytochrome b6-f complex subunit 6
Seq:
Struc:
31 a.a.
31 a.a.
Protein chain
Pfam   ArchSchema ?
P0A3Y1  (PETM_NOSS1) -  Cytochrome b6-f complex subunit 7
Seq:
Struc:
34 a.a.
32 a.a.
Protein chain
Pfam   ArchSchema ?
P58246  (PETG_NOSS1) -  Cytochrome b6-f complex subunit 5
Seq:
Struc:
37 a.a.
37 a.a.
Protein chain
Pfam   ArchSchema ?
P61048  (PETN_NOSS1) -  Cytochrome b6-f complex subunit 8
Seq:
Struc:
29 a.a.
29 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain D: E.C.1.10.9.1  - Plastoquinol--plastocyanin reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Plastoquinol + 2 oxidized plastocyanin + 2 H+(Side 1) = plastoquinone + 2 reduced plastocyanin + 4 H+(Side 2)
Plastoquinol
+ 2 × oxidized plastocyanin
+ 2 × H(+)(Side 1)
= plastoquinone
+ 2 × reduced plastocyanin
+ 4 × H(+)(Side 2)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   6 terms 
  Biological process     oxidation-reduction process   7 terms 
  Biochemical function     electron carrier activity     12 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M809196200 J Biol Chem 284:9861-9869 (2009)
PubMed id: 19189962  
 
 
Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120.
D.Baniulis, E.Yamashita, J.P.Whitelegge, A.I.Zatsman, M.P.Hendrich, S.S.Hasan, C.M.Ryan, W.A.Cramer.
 
  ABSTRACT  
 
The crystal structure of the cyanobacterial cytochrome b(6)f complex has previously been solved to 3.0-A resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b(6)f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical to those in the M. laminosus b(6)f complex. Purified b(6)f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b(6)f complex, determined to a resolution of 3.0A (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme b(p) that is rotated 180 degrees about the alpha- and gamma-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme c(n) is similar to that previously found in the b(6)f complex from other sources.
 
  Selected figure(s)  
 
Figure 1.
Density centrifugation of Nostoc cytochrome b[6]f fractions collected from the hydrophobic chromatography column. The two cytochrome b[6]f containing fractions, which eluted in the first fractions from the column (left), and in the late fractions (right), were concentrated, loaded onto 10-ml 8–35% sucrose gradient in the TNE buffer supplemented with 1 mm UDM, and centrifuged at 200,000 × g (16 h) in an SW-41 rotor (Beckman-Coulter). Cytochrome b[6]f monomer and dimer bands are indicated by arrows.
Figure 3.
Ribbon diagram of the symmetric dimeric structure of the cytochrome b[6]f complex from Nostoc sp. PCC 7120 determined from the 3.0-Å structure. The color code for the p-side of complex are: red, cyt f (petA); yellow, Rieske ISP (petA); blue, cytb (petB); purple, subunit IV; and green, petG, -L, -M, and -N. p-side heme of cyt f and [2Fe-2S] cluster are shown, along with two trans-membrane b-hemes, n-side heme c[n] represented as stick diagrams. The bound chlorophyll a and β-carotene are shown in stick format, in dark green and in orange, respectively. The inset shows bipyramidal crystals of the b[6]f complex from Nostoc obtained using the hanging drop, vapor-diffusion method described under “Experimental Procedures” (bar size, 100 μm).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 9861-9869) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21114674 R.Szymańska, J.Dłużewska, I.Slesak, and J.Kruk (2011).
Ferredoxin:NADP+ oxidoreductase bound to cytochrome b₆f complex is active in plastoquinone reduction: implications for cyclic electron transport.
  Physiol Plant, 141, 289-298.  
20237831 C.Dreher, R.Hielscher, A.Prodöhl, P.Hellwig, and D.Schneider (2010).
Characterization of two cytochrome b6 proteins from the cyanobacterium Gloeobacter violaceus PCC 7421.
  J Bioenerg Biomembr, 42, 517-526.  
19689132 A.I.Twigg, D.Baniulis, W.A.Cramer, and M.P.Hendrich (2009).
EPR detection of an O(2) surrogate bound to heme c(n) of the cytochrome b(6)f complex.
  J Am Chem Soc, 131, 12536-12537.  
19478086 A.de Lacroix de Lavalette, L.Barucq, J.Alric, F.Rappaport, and F.Zito (2009).
Is the redox state of the ci heme of the cytochrome b6f complex dependent on the occupation and structure of the Qi site and vice versa?
  J Biol Chem, 284, 20822-20829.  
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.