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PDBsum entry 2w2x

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protein ligands metals Protein-protein interface(s) links
Signaling protein/hydrolase PDB id
2w2x
Jmol
Contents
Protein chains
177 a.a. *
109 a.a. *
Ligands
GSP ×2
Metals
_MG ×2
Waters ×37
* Residue conservation analysis
PDB id:
2w2x
Name: Signaling protein/hydrolase
Title: Complex of rac2 and plcg2 spph domain
Structure: Ras-related c3 botulinum toxin substrate 2. Chain: a, b. Fragment: residues 2-179. Synonym: p21-rac2, small g protein, gx, rac2. Engineered: yes. Mutation: yes. 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2. Chain: c.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.
Resolution:
2.30Å     R-factor:   0.237     R-free:   0.294
Authors: O.Opaleye,T.D.Bunney,S.M.Roe,L.H.Pearl
Key ref:
T.D.Bunney et al. (2009). Structural insights into formation of an active signaling complex between Rac and phospholipase C gamma 2. Mol Cell, 34, 223-233. PubMed id: 19394299 DOI: 10.1016/j.molcel.2009.02.023
Date:
04-Nov-08     Release date:   05-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15153  (RAC2_HUMAN) -  Ras-related C3 botulinum toxin substrate 2
Seq:
Struc:
192 a.a.
177 a.a.*
Protein chains
Pfam   ArchSchema ?
P16885  (PLCG2_HUMAN) -  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1265 a.a.
109 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 38 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains C, D: E.C.3.1.4.11  - Phosphoinositide phospholipase C.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
myo-Inositol Phosphate Metabolism
      Reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1D-myo-inositol 1,4,5-trisphosphate + diacylglycerol
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
+ H(2)O
= 1D-myo-inositol 1,4,5-trisphosphate
+ diacylglycerol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   7 terms 
  Biological process     intracellular signal transduction   15 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.molcel.2009.02.023 Mol Cell 34:223-233 (2009)
PubMed id: 19394299  
 
 
Structural insights into formation of an active signaling complex between Rac and phospholipase C gamma 2.
T.D.Bunney, O.Opaleye, S.M.Roe, P.Vatter, R.W.Baxendale, C.Walliser, K.L.Everett, M.B.Josephs, C.Christow, F.Rodrigues-Lima, P.Gierschik, L.H.Pearl, M.Katan.
 
  ABSTRACT  
 
Rho family GTPases are important cellular switches and control a number of physiological functions. Understanding the molecular basis of interaction of these GTPases with their effectors is crucial in understanding their functions in the cell. Here we present the crystal structure of the complex of Rac2 bound to the split pleckstrin homology (spPH) domain of phospholipase C-gamma(2) (PLCgamma(2)). Based on this structure, we illustrate distinct requirements for PLCgamma(2) activation by Rac and EGF and generate Rac effector mutants that specifically block activation of PLCgamma(2), but not the related PLCbeta(2) isoform. Furthermore, in addition to the complex, we report the crystal structures of free spPH and Rac2 bound to GDP and GTPgammaS. These structures illustrate a mechanism of conformational switches that accompany formation of signaling active complexes and highlight the role of effector binding as a common feature of Rac and Cdc42 interactions with a variety of effectors.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal Structure of the Rac2^G12V(GTPγS)/PLCγ[2]spPH Complex
Domain organization of PLCγ[2] (A) shows domains common to all families (nPH, EF-hands, catalytic, and C2) and domains specific to PLCγ family (nSH2, cSH2, SH3, and spPH); spPH is shown in orange. Overview of the Rac2^G12V(2-177) GTPγS/PLCγ[2]spPH complex structure (B). Surface topology (shown as translucent surfaces) and ribbon representation of the complex show the spPH domain in orange and the Rac2 molecule in blue. The Rac2 switch I region is shown in green, and the switch II region is shown in magenta. The GTPγS molecule bound to Rac2 is in ball-and-stick representation. Close-up of the interaction interface is viewed from the side with important amino acid residues of both Rac2 and spPH represented as ball and sticks (C). Also shown is a close-up from above with important Rac2 amino acid residues (ball-and-stick representation) and the spPH surface (D). The hydrophobic cleft into which Rac2 residues Val36 and Phe37 protrude can be clearly seen. The summary of interactions at the interface is illustrated schematically highlighting the predominant types of bonding between the two species in the complex (E).
Figure 6.
Figure 6. Effector-Facilitated Conformational Changes in Rac/Cdc42 Proteins
Comparison of switch I regions of uncomplexed, GTP analog-bound Ras (pdb: 121P) (A) with an overlay of Rac2 and Cdc42 uncomplexed, GTP analog-bound structures (pdb: 2w2v and 2QRZ) ([B], left) and Rac2 and Cdc42 GTP analog-bound structures (overlay) from complexes with PLCγ[2] (pdb: 2w2x) and Par6 (pdb: 1NF3), respectively ([B], right). Conformations of switch I region and orientation of indicated key residues in free Rac/CDC42-(GTP) proteins and in complexes with their effectors are clearly different. Binding of several effectors to Rac/Cdc42 proteins involves interaction with switch I residues Val36 and Phe37 that stabilizes signaling-active (state 2) conformation where other switch I residues, Thr35 and Tyr32, can coordinate γ-phosphate of GTP.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2009, 34, 223-233) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20870410 T.D.Bunney, and M.Katan (2011).
PLC regulation: emerging pictures for molecular mechanisms.
  Trends Biochem Sci, 36, 88-96.  
20700106 J.A.Kenniston, and M.A.Lemmon (2010).
Dynamin GTPase regulation is altered by PH domain mutations found in centronuclear myopathy patients.
  EMBO J, 29, 3054-3067.  
20559679 K.Kwiatkowska (2010).
One lipid, multiple functions: how various pools of PI(4,5)P(2) are created in the plasma membrane.
  Cell Mol Life Sci, 67, 3927-3946.  
20062059 M.Yamashita, K.Kurokawa, Y.Sato, A.Yamagata, H.Mimura, A.Yoshikawa, K.Sato, A.Nakano, and S.Fukai (2010).
Structural basis for the Rho- and phosphoinositide-dependent localization of the exocyst subunit Sec3.
  Nat Struct Mol Biol, 17, 180-186.
PDB code: 3a58
19531496 K.L.Everett, T.D.Bunney, Y.Yoon, F.Rodrigues-Lima, R.Harris, P.C.Driscoll, K.Abe, H.Fuchs, M.H.de Angelis, P.Yu, W.Cho, and M.Katan (2009).
Characterization of phospholipase C gamma enzymes with gain-of-function mutations.
  J Biol Chem, 284, 23083-23093.  
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.