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PDBsum entry 1jo8
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Structural protein PDB id
1jo8

 

 

 

 

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Contents
Protein chain
58 a.a. *
Ligands
SO4 ×2
Waters ×131
* Residue conservation analysis
PDB id:
1jo8
Name: Structural protein
Title: Structural analysis of the yeast actin binding protein abp1 sh3 domain
Structure: Actin binding protein. Chain: a. Fragment: sh3 domain. Synonym: abp1p. Actin-binding protein abp1. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.30Å     R-factor:   0.145     R-free:   0.178
Authors: B.Fazi,M.J.Cope,A.Douangamath,S.Ferracuti,K.Schirwitz,A.Zucconi, D.G.Drubin,M.Wilmanns,G.Cesareni,L.Castagnoli
Key ref:
B.Fazi et al. (2002). Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis. J Biol Chem, 277, 5290-5298. PubMed id: 11668184 DOI: 10.1074/jbc.M109848200
Date:
27-Jul-01     Release date:   01-Mar-02    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15891  (ABP1_YEAST) -  Actin-binding protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		592 a.a.
58 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1074/jbc.M109848200 J Biol Chem 277:5290-5298 (2002)
PubMed id: 11668184  
 
 
Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis.
B.Fazi, M.J.Cope, A.Douangamath, S.Ferracuti, K.Schirwitz, A.Zucconi, D.G.Drubin, M.Wilmanns, G.Cesareni, L.Castagnoli.
 
  ABSTRACT  
 
Abp1p is an actin-binding protein that plays a central role in the organization of Saccharomyces cerevisiae actin cytoskeleton. By a combination of two-hybrid and phage-display approaches, we have identified six new ligands of the Abp1-SH3 domain. None of these SH3-mediated novel interactions was detected in recent all genome high throughput protein interaction projects. Here we show that the SH3-mediated association of Abp1p with the Ser/Thr kinases Prk1p and Ark1p is essential for their localization to actin cortical patches. The Abp1-SH3 domain has a rather unusual binding specificity, because its target peptides contain the tetrapentapeptide +XXXPXXPX+PXXL with positive charges flanking the polyproline core on both sides. Here we present the structure of the Abp1-SH3 domain solved at 1.3-A resolution. The peptide-binding pockets in the SH3 domain are flanked by two acidic residues that are uncommon at those positions in the SH3 domain family. We have shown by site-directed mutagenesis that one of these negatively charged side chains may be the key determinant for the preference for non-classical ligands.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Localization of Prk1p to actin cortical patches depends on an intact polyproline motif at its C terminus. Yeast cells were transfected with plasmids directing the synthesis of GFP-Prk1p (upper panel, PRK1) or GFP-Prk1p carrying a mutation in the polyproline stretch (lower panel, PRK1 mut poly P). In the panels on the left, the clear spots are attributed to fluorescence of the GFP-Prk1p hybrid protein. Actin was visualized in the two panels on the right by staining with rhodamine-conjugated phalloidin (Rh). To avoid disturbing cell physiology by overexpressing the Prk1p kinase, a mutationally inactivated kinase was used in this experiment (GFP-Prk1p K56A). 		Figure 5.
Fig. 5. Superposition of the Abp1p-SH3 domain (red) with Sem5-SH3 (green) and c-Abl-SH3 (blue). The residues in the Abp1-SH3-PXXP-binding site are labeled. They overlap almost perfectly to those in Sem5-SH3 and c-Abl-SH3. The figure was produced using MOLSCRIPT (49). Y53, Tyr-53; Y9, Tyr-9; W35, Trp-35; N52, Asn-52; Y7, Tyr-7; P50, Pro-50.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 5290-5298) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22113616 J.S.McLellan, M.Pancera, C.Carrico, J.Gorman, J.P.Julien, R.Khayat, R.Louder, R.Pejchal, M.Sastry, K.Dai, S.O'Dell, N.Patel, S.Shahzad-ul-Hussan, Y.Yang, B.Zhang, T.Zhou, J.Zhu, J.C.Boyington, G.Y.Chuang, D.Diwanji, I.Georgiev, Y.D.Kwon, D.Lee, M.K.Louder, S.Moquin, S.D.Schmidt, Z.Y.Yang, M.Bonsignori, J.A.Crump, S.H.Kapiga, N.E.Sam, B.F.Haynes, D.R.Burton, W.C.Koff, L.M.Walker, S.Phogat, R.Wyatt, J.Orwenyo, L.X.Wang, J.Arthos, C.A.Bewley, J.R.Mascola, G.J.Nabel, W.R.Schief, A.B.Ward, I.A.Wilson, and P.D.Kwong (2011).
Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
  Nature, 480, 336-343.
PDB codes: 3tcl 3u1s 3u2s 3u36 3u46 3u4b 3u4e
21232959 J.Schymeinsky, M.Sperandio, and B.Walzog (2011).
The mammalian actin-binding protein 1 (mAbp1): a novel molecular player in leukocyte biology.
  Trends Cell Biol, 21, 247-255.  
20696393 P.Robustelli, K.Kohlhoff, A.Cavalli, and M.Vendruscolo (2010).
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.
  Structure, 18, 923-933.  
20200225 R.Dieckmann, Y.von Heyden, C.Kistler, N.Gopaldass, S.Hausherr, S.W.Crawley, E.C.Schwarz, R.P.Diensthuber, G.P.Côté, G.Tsiavaliaris, and T.Soldati (2010).
A myosin IK-Abp1-PakB circuit acts as a switch to regulate phagocytosis efficiency.
  Mol Biol Cell, 21, 1505-1518.  
18939955 B.Huang, L.L.Chua, N.Bose, and M.Cai (2009).
Negative regulation of the actin-regulating kinase Prk1p by patch localization-induced autophosphorylation.
  Traffic, 10, 35-41.  
19590096 E.J.Stollar, B.Garcia, P.A.Chong, A.Rath, H.Lin, J.D.Forman-Kay, and A.R.Davidson (2009).
Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p.
  J Biol Chem, 284, 26918-26927.
PDB code: 2rpn
19176519 H.Wang, B.Kakaradov, S.R.Collins, L.Karotki, D.Fiedler, M.Shales, K.M.Shokat, T.C.Walther, N.J.Krogan, and D.Koller (2009).
A complex-based reconstruction of the Saccharomyces cerevisiae interactome.
  Mol Cell Proteomics, 8, 1361-1381.  
19217430 M.Chesarone, C.J.Gould, J.B.Moseley, and B.L.Goode (2009).
Displacement of formins from growing barbed ends by bud14 is critical for actin cable architecture and function.
  Dev Cell, 16, 292-302.  
18701694 A.A.Rodal, R.N.Motola-Barnes, and J.T.Littleton (2008).
Nervous wreck and Cdc42 cooperate to regulate endocytic actin assembly during synaptic growth.
  J Neurosci, 28, 8316-8325.  
18298676 C.P.Toret, L.Lee, M.Sekiya-Kawasaki, and D.G.Drubin (2008).
Multiple pathways regulate endocytic coat disassembly in Saccharomyces cerevisiae for optimal downstream trafficking.
  Traffic, 9, 848-859.  
18606003 J.Chen, H.Liang, and A.Fernández (2008).
Protein structure protection commits gene expression patterns.
  Genome Biol, 9, R107.  
17978096 M.Jin, and M.Cai (2008).
A Novel Function of Arp2p in Mediating Prk1p-specific Regulation of Actin and Endocytosis in Yeast.
  Mol Biol Cell, 19, 297-307.  
18701719 P.Vallurupalli, D.F.Hansen, and L.E.Kay (2008).
Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy.
  Proc Natl Acad Sci U S A, 105, 11766-11771.
PDB code: 2k3b
17898076 G.Zeng, B.Huang, S.P.Neo, J.Wang, and M.Cai (2007).
Scd5p mediates phosphoregulation of actin and endocytosis by the type 1 phosphatase Glc7p in yeast.
  Mol Biol Cell, 18, 4885-4898.  
17409071 J.Haynes, B.Garcia, E.J.Stollar, A.Rath, B.J.Andrews, and A.R.Davidson (2007).
The biologically relevant targets and binding affinity requirements for the function of the yeast actin-binding protein 1 Src-homology 3 domain vary with genetic context.
  Genetics, 176, 193-208.  
17452534 Y.Sun, S.Carroll, M.Kaksonen, J.Y.Toshima, and D.G.Drubin (2007).
PtdIns(4,5)P2 turnover is required for multiple stages during clathrin- and actin-dependent endocytic internalization.
  J Cell Biol, 177, 355-367.  
16373478 A.Zarrine-Afsar, A.Mittermaier, L.E.Kay, and A.R.Davidson (2006).
Protein stabilization by specific binding of guanidinium to a functional arginine-binding surface on an SH3 domain.
  Protein Sci, 15, 162-170.  
16959963 J.B.Moseley, and B.L.Goode (2006).
The yeast actin cytoskeleton: from cellular function to biochemical mechanism.
  Microbiol Mol Biol Rev, 70, 605-645.  
16802101 K.Hertveldt, J.Robben, and G.Volckaert (2006).
Whole genome phage display selects for proline-rich Boi polypeptides against Bem1p.
  Biotechnol Lett, 28, 1233-1239.  
15798181 C.J.Stefan, S.M.Padilla, A.Audhya, and S.D.Emr (2005).
The phosphoinositide phosphatase Sjl2 is recruited to cortical actin patches in the control of vesicle formation and fission during endocytosis.
  Mol Cell Biol, 25, 2910-2923.  
16155203 F.Bauer, K.Schweimer, H.Meiselbach, S.Hoffmann, P.Rösch, and H.Sticht (2005).
Structural characterization of Lyn-SH3 domain in complex with a herpesviral protein reveals an extended recognition motif that enhances binding affinity.
  Protein Sci, 14, 2487-2498.
PDB code: 1w1f
15381149 G.Zeng, and M.Cai (2005).
Prk1p.
  Int J Biochem Cell Biol, 37, 48-53.  
15872087 O.Quintero-Monzon, A.A.Rodal, B.Strokopytov, S.C.Almo, and B.L.Goode (2005).
Structural and functional dissection of the Abp1 ADFH actin-binding domain reveals versatile in vivo adapter functions.
  Mol Biol Cell, 16, 3128-3139.  
14737190 C.Landgraf, S.Panni, L.Montecchi-Palazzi, L.Castagnoli, J.Schneider-Mergener, R.Volkmer-Engert, and G.Cesareni (2004).
Protein interaction networks by proteome peptide scanning.
  PLoS Biol, 2, E14.  
14978303 M.R.Ferguson, X.Fan, M.Mukherjee, J.Luo, R.Khan, J.C.Ferreon, V.J.Hilser, R.E.Shope, and R.O.Fox (2004).
Directed discovery of bivalent peptide ligands to an SH3 domain.
  Protein Sci, 13, 626-632.  
12814545 A.A.Rodal, A.L.Manning, B.L.Goode, and D.G.Drubin (2003).
Negative regulation of yeast WASp by two SH3 domain-containing proteins.
  Curr Biol, 13, 1000-1008.  
14668868 A.Zarrinpar, S.H.Park, and W.A.Lim (2003).
Optimization of specificity in a cellular protein interaction network by negative selection.
  Nature, 426, 676-680.  
12634840 E.Smythe, and K.R.Ayscough (2003).
The Ark1/Prk1 family of protein kinases. Regulators of endocytosis and the actin skeleton.
  EMBO Rep, 4, 246-251.  
12547433 S.S.Sidhu, G.D.Bader, and C.Boone (2003).
Functional genomics of intracellular peptide recognition domains with combinatorial biology methods.
  Curr Opin Chem Biol, 7, 97.  
12512072 S.S.Sidhu, W.J.Fairbrother, and K.Deshayes (2003).
Exploring protein-protein interactions with phage display.
  Chembiochem, 4, 14-25.  
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.

 

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