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PDBsum entry 2pk9

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protein ligands Protein-protein interface(s) links
Signaling protein,transferase/cell cycle PDB id
2pk9
Jmol
Contents
Protein chains
287 a.a. *
214 a.a. *
266 a.a. *
Ligands
MES ×2
* Residue conservation analysis
PDB id:
2pk9
Name: Signaling protein,transferase/cell cycle
Title: Structure of the pho85-pho80 cdk-cyclin complex of the phosphate-responsive signal transduction pathway
Structure: Cyclin-dependent protein kinase pho85. Chain: a, c. Synonym: serine/threonine-protein kinase pho85. Negative regulator of the pho system. Engineered: yes. Pho85 cyclin pho80. Chain: b, d. Synonym: phosphate system cyclin pho80. Aminoglycoside antibiotic sensitivity protein 3.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: pho85, ssg3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: pho80, ags3, tup7, vac5.
Resolution:
2.91Å     R-factor:   0.283     R-free:   0.315
Authors: K.Huang,I.Ferrin-O'Connell,W.Zhang,G.A.Leonard,E.K.O'Shea, F.A.Quiocho
Key ref:
K.Huang et al. (2007). Structure of the Pho85-Pho80 CDK-cyclin complex of the phosphate-responsive signal transduction pathway. Mol Cell, 28, 614-623. PubMed id: 18042456 DOI: 10.1016/j.molcel.2007.09.013
Date:
17-Apr-07     Release date:   11-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17157  (PHO85_YEAST) -  Cyclin-dependent protein kinase PHO85
Seq:
Struc:
305 a.a.
287 a.a.
Protein chains
Pfam   ArchSchema ?
P20052  (PHO80_YEAST) -  PHO85 cyclin PHO80
Seq:
Struc:
293 a.a.
214 a.a.
Protein chain
Pfam   ArchSchema ?
P17157  (PHO85_YEAST) -  Cyclin-dependent protein kinase PHO85
Seq:
Struc:
305 a.a.
266 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, C: E.C.2.7.11.22  - Cyclin-dependent kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
= ADP
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cyclin-dependent protein kinase holoenzyme complex   3 terms 
  Biological process     response to DNA damage stimulus   17 terms 
  Biochemical function     nucleotide binding     11 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.molcel.2007.09.013 Mol Cell 28:614-623 (2007)
PubMed id: 18042456  
 
 
Structure of the Pho85-Pho80 CDK-cyclin complex of the phosphate-responsive signal transduction pathway.
K.Huang, I.Ferrin-O'Connell, W.Zhang, G.A.Leonard, E.K.O'Shea, F.A.Quiocho.
 
  ABSTRACT  
 
The ability to sense and respond appropriately to environmental changes is a primary requirement of all living organisms. In response to phosphate limitation, Saccharomyces cerevisiae induces transcription of a set of genes involved in the regulation of phosphate acquisition from the ambient environment. A signal transduction pathway (the PHO pathway) mediates this response, with Pho85-Pho80 playing a vital role. Here we report the X-ray structure of Pho85-Pho80, a prototypic structure of a CDK-cyclin complex functioning in transcriptional regulation in response to environmental changes. The structure revealed a specific salt link between a Pho85 arginine and a Pho80 aspartate that makes phosphorylation of the Pho85 activation loop dispensable and that maintains a Pho80 loop conformation for possible substrate recognition. It further showed two sites on the Pho80 cyclin for high-affinity binding of the transcription factor substrate (Pho4) and the CDK inhibitor (Pho81) that are markedly distant to each other and the active site.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A Salt Link between Pho85 R132 and Pho80 D136 that Makes T Loop Phosphorylation Dispensable
(A) Relative positions of the loop between α3 and α4 in Pho80 (red) and cyclin A (gray) and the PSTAIRE helices and segments of the activation loops in Pho85 (residues 155–168) (marine) and phosphorylated (T160) CDK2 (residues 149–163) (green). The overlay is based on the superposition of the structures of the kinase subunits as they occur in the structures of the Pho85-Pho80-ATP-γ-S complex, and the phosphorylated CDK2-cyclin A complex (Brown et al., 1999). The α3-α4 loop in Pho80 deploys D136, hence the “D loop” name. The activation loop T160 (with the phosphoryl adduct) of CDK2 corresponds to S166 in Pho85. Pho85 R132 and CDK2 R126 are superimposable. CDK5 R125 adopts an almost identical position as those of Pho85 R132 and CDK2 R126 (data not shown). Pho80 D136 has no counterpart in cyclin A and p25. A more global view of the D loop and the salt link is shown in Figure 1A.
(B) Similar superposition as shown in (A), except that the CDK2 structure is the unphosphorylated form (Jeffrey et al., 1995). The position of R126 of CDK2 is essentially unchanged from that in the phosphorylated CDK2 (A). Note the significant change in the conformation of the segment of the T loop of CDK2 following phosphorylation (compare with that in [A]).
Figure 3.
Figure 3. Three Functional Sites of the Pho80 Cyclin Subunit
(A) Ribbon trace of Pho80. The regions of the three functional sites are identified as follows (see also text): the bound ATP-γ-S (stick representation) marking the location of the kinase active-site region; the cluster of residues C30, L38, R41, M42, and G229 and segments of residues 17–24 and 243–246 forming a large cavity for possible tight interaction with the site on Pho4 distal to the phosphorylatable sites; and the salt link between R121 and E154 in a region for docking the inhibitor, Pho81. The peptide near the ATP-γ-S corresponds to a model of the the SPRL consensus sequence of the five Pho4 phosphorylation sites (O'Neill et al., 1996). Placement of the peptide was derived by superimposing the atomic coordinates of only the Pho85 and CDK2 subunits in the Pho85-Pho80-ATP-γ-S structure and the structure of the phosphorylated CDK2-cyclin A with a bound peptide containing the SPRK consensus sequence and AMPPNP-Mg^2+ (Brown et al., 1999). Changing the K at the +3 position to L to conform to the Pho4 consensus sequence, SPXI/L, indicates that the L side chain would be within van der Waals distance to the F138 located on the α3-α4 (or D) loop in Pho80.
(B) Electrostatic surface potential surface of Pho80 contoured at −10 kT (red) and +10 kT (blue) calculated with GRASP (Nicholls et al., 1991). Pho80 is in identical orientation as in (A). The region involved in binding of the CKI Pho81 is enclosed by red dashed lines. The region involved in docking of the site on Pho4 distal to the phosphorylation sites is enclosed in magenta dashed lines.
(C) Hydrophobic patch on cyclin A for docking the RXL motif of substrates or CKIs. The bound ligand, with backbone trace in green, shows only the RRL sequence (the equivalent of the RXL motif) of the substrate recruitment peptide RRLFGE of p107 (Brown et al., 1999). The residues M210, I213, and E220 on α1 and R250 on α3 define the specificity of the patch in a group of cell-cycle cyclins for the RXL motif (Endicott et al., 1999).
(D) Identical to (C), but with the surface of cyclin A removed for clarity, and the α1 and α3 helices and their preceding loops of Pho80 superimposed. The first two turns of α1 of cyclin A, which provides M210 and I213, are missing in the corresponding α1 of Pho80.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2007, 28, 614-623) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20054690 B.Smets, R.Ghillebert, P.De Snijder, M.Binda, E.Swinnen, C.De Virgilio, and J.Winderickx (2010).
Life in the midst of scarcity: adaptations to nutrient availability in Saccharomyces cerevisiae.
  Curr Genet, 56, 1.  
19218424 K.Streckfuss-Bömeke, F.Schulze, B.Herzog, E.Scholz, and G.H.Braus (2009).
Degradation of Saccharomyces cerevisiae transcription factor Gcn4 requires a C-terminal nuclear localization signal in the cyclin Pcl5.
  Eukaryot Cell, 8, 496-510.  
18794371 S.Aviram, E.Simon, T.Gildor, F.Glaser, and D.Kornitzer (2008).
Autophosphorylation-induced degradation of the Pho85 cyclin Pcl5 is essential for response to amino acid limitation.
  Mol Cell Biol, 28, 6858-6869.  
18566585 S.Baumli, G.Lolli, E.D.Lowe, S.Troiani, L.Rusconi, A.N.Bullock, J.E.Debreczeni, S.Knapp, and L.N.Johnson (2008).
The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation.
  EMBO J, 27, 1907-1918.
PDB codes: 2ivx 3blh 3blq 3blr
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