spacer
spacer

PDBsum entry 2v6v
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Regulator PDB id
2v6v

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
135 a.a. *
Ligands
DTT
Waters ×439
* Residue conservation analysis
PDB id:
2v6v
Name: Regulator
Title: The structure of the bem1p px domain
Structure: Bud emergence protein 1. Chain: a, b. Fragment: px domain, residues 266-413. Synonym: bem1p, suppressor of rho3 protein 1. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.50Å     R-factor:   0.224     R-free:   0.256
Authors: R.V.Stahelin,D.Karathanassis,D.Murray,R.L.Williams,W.Cho
Key ref:
R.V.Stahelin et al. (2007). Structural and membrane binding analysis of the Phox homology domain of Bem1p: basis of phosphatidylinositol 4-phosphate specificity. J Biol Chem, 282, 25737-25747. PubMed id: 17581820 DOI: 10.1074/jbc.M702861200
Date:
21-Jul-07     Release date:   31-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P29366  (BEM1_YEAST) -  Bud emergence protein 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		551 a.a.
135 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1074/jbc.M702861200 J Biol Chem 282:25737-25747 (2007)
PubMed id: 17581820  
 
 
Structural and membrane binding analysis of the Phox homology domain of Bem1p: basis of phosphatidylinositol 4-phosphate specificity.
R.V.Stahelin, D.Karathanassis, D.Murray, R.L.Williams, W.Cho.
 
  ABSTRACT  
 
Phox homology (PX) domains, which have been identified in a variety of proteins involved in cell signaling and membrane trafficking, have been shown to interact with phosphoinositides (PIs) with different affinities and specificities. To elucidate the structural origin of the diverse PI specificity of PX domains, we determined the crystal structure of the PX domain from Bem1p that has been reported to bind phosphatidylinositol 4-phosphate (PtdIns(4)P). We also measured the membrane binding properties of the PX domain and its mutants by surface plasmon resonance and monolayer techniques and calculated the electrostatic potentials for the PX domain in the absence and presence of bound PtdIns(4)P. The Bem1p PX domain contains a signature PI-binding site optimized for PtdIns(4)P binding and also harbors basic and hydrophobic residues on the membrane-binding surface. The membrane binding of the Bem1p PX domain is initiated by nonspecific electrostatic interactions between the cationic membrane-binding surface of the domain and anionic membrane surfaces, followed by the membrane penetration of hydrophobic residues. Unlike other PX domains, the Bem1p PX domain has high intrinsic membrane penetrating activity in the absence of PtdIns(4)P, suggesting that the partial membrane penetration may occur before specific PtdIns(4)P binding and last after the removal of PtdIns(4)P under certain conditions. This structural and functional study of the PtdIns(4)P-binding Bem1p PX domain provides new insight into the diverse PI specificities and membrane-binding mechanisms of PX domains.
 
  Selected figure(s)  
 
Figure 4.
Monolayer penetration of the Bem1p PX and OSBP and FAPP1 PH domains into various phospholipids.A, Δπ was measured as a function of π[0] for wild-type Bem1p-PX with POPC/POPE (80:20) (○), POPC/POPE/PtdIns(4)P (77:20:3) (•), POPC/POPE/PtdIns(3)P (77:20:3) (▪), POPC/POPE/PtdIns(5)P (77:20:3) (▴), and POPC/POPE/POPS (60:20:20) (□) monolayers. B, Bem1p (○), OSBP (□), and FAPP1 (▵) were allowed interact with the POPC/POPE (80:20) monolayer, or Bem1p (•), OSBP (▪), and FAPP1 (▴) were added to the POPC/POPE/PtdIns(4)P (77:20:3) monolayer. The subphase consisted of 10 mm HEPES (pH 7.4) containing 0.16 m KCl. n = 2. 		Figure 6.
Bem1p PX domain in the absence and presence of PS and PtdIns(4)P.A, C, and E show the electrostatic potential mapped to the membrane-binding surface of the PX domain. B, D, and F represent the PX domain as a C-α backbone and the electrostatic potential as a two-dimensional contour. The molecules are rotated 90° forward from A, C, and E, and the membrane-binding surfaces point downward in this orientation. Even in the absence of lipids (A and B), Tyr^360 is exposed over the electrostatic potential surface, accounting for the high intrinsic membrane penetrating activity of Bem1p-PX. Upon binding to PS (C and D), the electrostatic potential of the membrane-binding surface of Bem1p-PX is relatively unchanged. Upon binding to PtdIns(4)P (E and F), the positive electrostatic potential of the membrane-binding surface of Bem1p-PX is greatly decreased, exposing Trp^346, which will further penetrate into the membrane. PtdIns(4)P is colored yellow, and Trp^346 and Tyr^360 are colored green. PS is not shown.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 25737-25747) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21145462 K.Moravcevic, J.M.Mendrola, K.R.Schmitz, Y.H.Wang, D.Slochower, P.A.Janmey, and M.A.Lemmon (2010).
Kinase associated-1 domains drive MARK/PAR1 kinases to membrane targets by binding acidic phospholipids.
  Cell, 143, 966-977.
PDB codes: 3ose 3osm 3ost
20300118 M.Lenoir, U.Coskun, M.Grzybek, X.Cao, S.B.Buschhorn, J.James, K.Simons, and M.Overduin (2010).
Structural basis of wedging the Golgi membrane by FAPP pleckstrin homology domains.
  EMBO Rep, 11, 279-284.  
20122178 S.Banerjee, S.Basu, and S.Sarkar (2010).
Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages.
  BMC Genomics, 11, 83.  
20616805 S.Schoebel, W.Blankenfeldt, R.S.Goody, and A.Itzen (2010).
High-affinity binding of phosphatidylinositol 4-phosphate by Legionella pneumophila DrrA.
  EMBO Rep, 11, 598-604.
PDB code: 3n6o
20559318 T.G.Kutateladze (2010).
Translation of the phosphoinositide code by PI effectors.
  Nat Chem Biol, 6, 507-513.  
19095644 E.Brombacher, S.Urwyler, C.Ragaz, S.S.Weber, K.Kami, M.Overduin, and H.Hilbi (2009).
Rab1 guanine nucleotide exchange factor SidM is a major phosphatidylinositol 4-phosphate-binding effector protein of Legionella pneumophila.
  J Biol Chem, 284, 4846-4856.  
19940249 X.Cao, U.Coskun, M.Rössle, S.B.Buschhorn, M.Grzybek, T.R.Dafforn, M.Lenoir, M.Overduin, and K.Simons (2009).
Golgi protein FAPP2 tubulates membranes.
  Proc Natl Acad Sci U S A, 106, 21121-21125.  
18312637 G.N.Parkinson, D.Vines, P.C.Driscoll, and S.Djordjevic (2008).
Crystal structures of PI3K-C2alpha PX domain indicate conformational change associated with ligand binding.
  BMC Struct Biol, 8, 13.
PDB codes: 2rea 2red
18672905 K.Shen, S.Sergeant, R.R.Hantgan, L.C.McPhail, and D.A.Horita (2008).
Mutations in the PX-SH3A linker of p47phox decouple PI(3,4)P2 binding from NADPH oxidase activation.
  Biochemistry, 47, 8855-8865.  
17900370 T.Kawahara, and J.D.Lambeth (2007).
Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes.
  BMC Evol Biol, 7, 178.  
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 codes are shown on the right.

 

spacer
spacer