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PDBsum entry 2b9h

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2b9h
Jmol
Contents
Protein chains
337 a.a. *
12 a.a. *
Ligands
ADP
Metals
_MG
Waters ×391
* Residue conservation analysis
PDB id:
2b9h
Name: Transferase
Title: Crystal structure of fus3 with a docking motif from ste7
Structure: Mitogen-activated protein kinase fus3. Chain: a. Synonym: map kinase fus3. Engineered: yes. Mutation: yes. Serine/threonine-protein kinase ste7. Chain: c. Fragment: ste7 docking motif. Synonym: ste7.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: fus3, dac2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the ste7 docking motif was chemically synthesized. The sequence of this peptide naturally exists
Biol. unit: Dimer (from PQS)
Resolution:
1.55Å     R-factor:   0.187     R-free:   0.216
Authors: A.Remenyi,M.C.Good,R.P.Bhattacharyya,W.A.Lim
Key ref:
A.Reményi et al. (2005). The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network. Mol Cell, 20, 951-962. PubMed id: 16364919 DOI: 10.1016/j.molcel.2005.10.030
Date:
11-Oct-05     Release date:   03-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16892  (FUS3_YEAST) -  Mitogen-activated protein kinase FUS3
Seq:
Struc:
353 a.a.
337 a.a.*
Protein chain
No UniProt id for this chain
Struc: 12 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.2.7.11.24  - Mitogen-activated protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   4 terms 
  Biological process     conjugation   13 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.molcel.2005.10.030 Mol Cell 20:951-962 (2005)
PubMed id: 16364919  
 
 
The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network.
A.Reményi, M.C.Good, R.P.Bhattacharyya, W.A.Lim.
 
  ABSTRACT  
 
Cells use a network of mitogen-activated protein kinases (MAPKs) to coordinate responses to diverse extracellular signals. Here, we examine the role of docking interactions in determining connectivity of the yeast MAPKs Fus3 and Kss1. These closely related kinases are activated by the common upstream MAPK kinase Ste7 yet generate distinct output responses, mating and filamentous growth, respectively. We find that docking interactions are necessary for communication with the kinases and that they can encode subtle differences in pathway-specific input and output. The cell cycle arrest mediator Far1, a mating-specific substrate, has a docking motif that selectively binds Fus3. In contrast, the shared partner Ste7 has a promiscuous motif that binds both Fus3 and Kss1. Structural analysis reveals that Fus3 interacts with specific and promiscuous peptides in conformationally distinct modes. Induced fit recognition may allow docking peptides to achieve discrimination by exploiting subtle differences in kinase flexibility.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Docking Motifs Found in Interaction Partners of the Saccharomyces cerevisiae MAPKs Fus3 and Kss1
Figure 3.
Figure 3. Structure of the Fus3 MAPK
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 20, 951-962) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22531118 C.F.Tiger, F.Krause, G.Cedersund, R.Palmér, E.Klipp, S.Hohmann, H.Kitano, and M.Krantz (2012).
A framework for mapping, visualisation and automatic model creation of signal-transduction networks.
  Mol Syst Biol, 8, 578.  
21551057 M.C.Good, J.G.Zalatan, and W.A.Lim (2011).
Scaffold proteins: hubs for controlling the flow of cellular information.
  Science, 332, 680-686.  
20019085 B.Raisley, H.N.Nguyen, and J.A.Hadwiger (2010).
G{alpha}5 subunit-mediated signalling requires a D-motif and the MAPK ERK1 in Dictyostelium.
  Microbiology, 156, 789-797.  
20454442 C.W.Li, and B.S.Chen (2010).
Identifying functional mechanisms of gene and protein regulatory networks in response to a broader range of environmental stresses.
  Comp Funct Genomics, (), 408705.  
20880736 H.Saito (2010).
Regulation of cross-talk in yeast MAPK signaling pathways.
  Curr Opin Microbiol, 13, 677-683.  
21134636 R.Akella, X.Min, Q.Wu, K.H.Gardner, and E.J.Goldsmith (2010).
The third conformation of p38α MAP kinase observed in phosphorylated p38α and in solution.
  Structure, 18, 1571-1578.
PDB code: 3p4k
21070949 W.Ma, Y.Shang, Z.Wei, W.Wen, W.Wang, and M.Zhang (2010).
Phosphorylation of DCC by ERK2 is facilitated by direct docking of the receptor P1 domain to the kinase.
  Structure, 18, 1502-1511.
PDB code: 3o71
19196711 A.J.Bardwell, E.Frankson, and L.Bardwell (2009).
Selectivity of docking sites in MAPK kinases.
  J Biol Chem, 284, 13165-13173.  
19295513 A.Mody, J.Weiner, and S.Ramanathan (2009).
Modularity of MAP kinases allows deformation of their signalling pathways.
  Nat Cell Biol, 11, 484-491.  
19526051 F.Xu, P.Du, H.Shen, H.Hu, Q.Wu, J.Xie, and L.Yu (2009).
Correlated mutation analysis on the catalytic domains of serine/threonine protein kinases.
  PLoS One, 4, e5913.  
19519955 G.L.Johnson, and S.M.Gomez (2009).
Sequence patches on MAPK surfaces define protein-protein interactions.
  Genome Biol, 10, 222.  
19765570 H.N.Nguyen, and J.A.Hadwiger (2009).
The Galpha4 G protein subunit interacts with the MAP kinase ERK2 using a D-motif that regulates developmental morphogenesis in Dictyostelium.
  Dev Biol, 335, 385-395.  
19424502 M.C.Balasu, L.N.Spiridon, S.Miron, C.T.Craescu, A.J.Scheidig, A.J.Petrescu, and S.E.Szedlacsek (2009).
Interface analysis of the complex between ERK2 and PTP-SL.
  PLoS ONE, 4, e5432.  
19303851 M.Good, G.Tang, J.Singleton, A.Reményi, and W.A.Lim (2009).
The Ste5 scaffold directs mating signaling by catalytically unlocking the Fus3 MAP kinase for activation.
  Cell, 136, 1085-1097.
PDB code: 3fze
19123063 M.J.Marín, M.Flández, C.Bermejo, J.Arroyo, H.Martín, and M.Molina (2009).
Different modulation of the outputs of yeast MAPK-mediated pathways by distinct stimuli and isoforms of the dual-specificity phosphatase Msg5.
  Mol Genet Genomics, 281, 345-359.  
20020052 R.B.Annan, A.Y.Lee, I.D.Reid, A.Sayad, M.Whiteway, M.Hallett, and D.Y.Thomas (2009).
A biochemical genomics screen for substrates of Ste20p kinase enables the in silico prediction of novel substrates.
  PLoS One, 4, e8279.  
19141286 X.Min, R.Akella, H.He, J.M.Humphreys, S.E.Tsutakawa, S.J.Lee, J.A.Tainer, M.H.Cobb, and E.J.Goldsmith (2009).
The structure of the MAP2K MEK6 reveals an autoinhibitory dimer.
  Structure, 17, 96.
PDB code: 3enm
18619997 M.S.Cortese, V.N.Uversky, and A.K.Dunker (2008).
Intrinsic disorder in scaffold proteins: getting more from less.
  Prog Biophys Mol Biol, 98, 85.  
18346117 P.Côte, and M.Whiteway (2008).
The role of Candida albicans FAR1 in regulation of pheromone-mediated mating, gene expression and cell cycle arrest.
  Mol Microbiol, 68, 392-404.  
18068683 R.Akella, T.M.Moon, and E.J.Goldsmith (2008).
Unique MAP Kinase binding sites.
  Biochim Biophys Acta, 1784, 48-55.  
18212044 Y.Murakami, K.Tatebayashi, and H.Saito (2008).
Two adjacent docking sites in the yeast Hog1 mitogen-activated protein (MAP) kinase differentially interact with the Pbs2 MAP kinase kinase and the Ptp2 protein tyrosine phosphatase.
  Mol Cell Biol, 28, 2481-2494.  
17952059 C.I.Maeder, M.A.Hink, A.Kinkhabwala, R.Mayr, P.I.Bastiaens, and M.Knop (2007).
Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling.
  Nat Cell Biol, 9, 1319-1326.  
17585314 J.A.Ubersax, and J.E.Ferrell (2007).
Mechanisms of specificity in protein phosphorylation.
  Nat Rev Mol Cell Biol, 8, 530-541.  
17711850 M.Jiménez-Sánchez, V.J.Cid, and M.Molina (2007).
Retrophosphorylation of Mkk1 and Mkk2 MAPKKs by the Slt2 MAPK in the yeast cell integrity pathway.
  J Biol Chem, 282, 31174-31185.  
17604854 R.E.Chen, and J.Thorner (2007).
Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae.
  Biochim Biophys Acta, 1773, 1311-1340.  
17570479 R.Linding, L.J.Jensen, G.J.Ostheimer, M.A.van Vugt, C.Jørgensen, I.M.Miron, F.Diella, K.Colwill, L.Taylor, K.Elder, P.Metalnikov, V.Nguyen, A.Pasculescu, J.Jin, J.G.Park, L.D.Samson, J.R.Woodgett, R.B.Russell, P.Bork, M.B.Yaffe, and T.Pawson (2007).
Systematic discovery of in vivo phosphorylation networks.
  Cell, 129, 1415-1426.  
16469909 A.Breitkreutz, and M.Tyers (2006).
Cell signaling. A sophisticated scaffold wields a new trick.
  Science, 311, 789-790.
PDB codes: 2f49 2fa2
17079133 A.Reményi, M.C.Good, and W.A.Lim (2006).
Docking interactions in protein kinase and phosphatase networks.
  Curr Opin Struct Biol, 16, 676-685.  
17046812 B.Zhou, J.Zhang, S.Liu, S.Reddy, F.Wang, and Z.Y.Zhang (2006).
Mapping ERK2-MKP3 binding interfaces by hydrogen/deuterium exchange mass spectrometry.
  J Biol Chem, 281, 38834-38844.  
16884917 L.Bardwell, and K.Shah (2006).
Analysis of mitogen-activated protein kinase activation and interactions with regulators and substrates.
  Methods, 40, 213-223.  
17052210 L.Bardwell (2006).
Mechanisms of MAPK signalling specificity.
  Biochem Soc Trans, 34, 837-841.  
16756506 R.P.Bhattacharyya, A.Reményi, B.J.Yeh, and W.A.Lim (2006).
Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits.
  Annu Rev Biochem, 75, 655-680.  
16424299 R.P.Bhattacharyya, A.Reményi, M.C.Good, C.J.Bashor, A.M.Falick, and W.A.Lim (2006).
The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway.
  Science, 311, 822-826.
PDB codes: 2f49 2f9g 2fa2
16765894 T.Zhou, L.Sun, J.Humphreys, and E.J.Goldsmith (2006).
Docking interactions induce exposure of activation loop in the MAP kinase ERK2.
  Structure, 14, 1011-1019.
PDB code: 2gph
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.