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PDBsum entry 3ci5

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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
3ci5
Jmol
Contents
Protein chains
368 a.a. *
126 a.a. *
Ligands
SO4 ×10
ATP
GOL ×5
Metals
_MG
_CA
Waters ×460
* Residue conservation analysis
PDB id:
3ci5
Name: Structural protein
Title: Complex of phosphorylated dictyostelium discoideum actin wit
Structure: Major actin. Chain: a. Gelsolin. Chain: g. Fragment: gelsolin segment 1 (unp residues 52-176). Synonym: actin-depolymerizing factor, adf, brevin, agel. Engineered: yes
Source: Dictyostelium discoideum. Slime mold. Homo sapiens. Human. Gene: gsn. Expressed in: escherichia coli.
Resolution:
1.70Å     R-factor:   0.143     R-free:   0.191
Authors: K.Baek,R.Dominguez
Key ref:
K.Baek et al. (2008). Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding. Proc Natl Acad Sci U S A, 105, 11748-11753. PubMed id: 18689676 DOI: 10.1073/pnas.0805852105
Date:
10-Mar-08     Release date:   19-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07830  (ACT1_DICDI) -  Major actin
Seq:
Struc:
376 a.a.
368 a.a.*
Protein chain
Pfam   ArchSchema ?
P06396  (GELS_HUMAN) -  Gelsolin
Seq:
Struc:
 
Seq:
Struc:
782 a.a.
126 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell-cell contact zone   12 terms 
  Biological process     macropinocytosis   12 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
DOI no: 10.1073/pnas.0805852105 Proc Natl Acad Sci U S A 105:11748-11753 (2008)
PubMed id: 18689676  
 
 
Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding.
K.Baek, X.Liu, F.Ferron, S.Shu, E.D.Korn, R.Dominguez.
 
  ABSTRACT  
 
On starvation, Dictyostelium cells aggregate to form multicellular fruiting bodies containing spores that germinate when transferred to nutrient-rich medium. This developmental cycle correlates with the extent of actin phosphorylation at Tyr-53 (pY53-actin), which is low in vegetative cells but high in viable mature spores. Here we describe high-resolution crystal structures of pY53-actin and unphosphorylated actin in complexes with gelsolin segment 1 and profilin. In the structure of pY53-actin, the phosphate group on Tyr-53 makes hydrogen-bonding interactions with residues of the DNase I-binding loop (D-loop) of actin, resulting in a more stable conformation of the D-loop than in the unphosphorylated structures. A more rigidly folded D-loop may explain some of the previously described properties of pY53-actin, including its increased critical concentration for polymerization, reduced rates of nucleation and pointed end elongation, and weak affinity for DNase I. We show here that phosphorylation of Tyr-53 inhibits subtilisin cleavage of the D-loop and reduces the rate of nucleotide exchange on actin. The structure of profilin-Dictyostelium-actin is strikingly similar to previously determined structures of profilin-beta-actin and profilin-alpha-actin. By comparing this representative set of profilin-actin structures with other structures of actin, we highlight the effects of profilin on the actin conformation. In the profilin-actin complexes, subdomains 1 and 3 of actin close around profilin, producing a 4.7 degrees rotation of the two major domains of actin relative to each other. As a result, the nucleotide cleft becomes moderately more open in the profilin-actin complex, probably explaining the stimulation of nucleotide exchange on actin by profilin.
 
  Selected figure(s)  
 
Figure 1.
Conformational change in actin subdomain 2 on phosphorylation of Tyr-53. (A and B) Close views of subdomain 2 in the structures of unphosphorylated actin and pY53-actin, showing omit electron density maps (contoured at 1 σ) around Tyr-53 (see Figs. S3 and S5 for a full view of the G1-actin structure). The D-loop was not visualized in the unphosphorylated structure. Hydrogen-bonding contacts (red dashed lines) between the oxygen atoms of the phosphate group on Tyr-53 and residues of the D-loop stabilize the conformation of the D-loop in the structure of pY53-actin. This and other figures of the paper were generated with the program PyMOL (http://pymol.sourceforge.net/). (C) Phosphorylation protects the D-loop from subtilisin cleavage, as shown by the ≈50% decrease in the initial rate of digestion. (D and E) Based on the increase in fluorescence as etheno-ATP replaces actin-bound ATP, phosphorylation reduces the rate of nucleotide exchange from 0.011 s^−1 for unphosphorylated actin to 0.006 s^−1 for pY53-actin, but profilin accelerates and gelsolin inhibits nucleotide exchange to the same extents for both forms of actin. The increase in fluorescence at equilibrium for pY53-actin is only 50% of the increase for unphosphorylated actin. Data were recorded every 10 s.
Figure 2.
Profilin binding causes a moderate opening of the nucleotide cleft in actin. (A) Superimposition of the structures of profilin–Dictyostelium-actin (blue and cyan) and uncomplexed monomeric actin (28) (blue and magenta). Two orientations are shown, rotated by 90°. The latter structure was obtained by mutagenesis in subdomain 4 and is thought to be free of perturbations resulting from the binding of an ABP or chemical cross-linking. For clarity, profilin is not shown in this figure (see Figs. S5 and S6 for a full view of the profilin–actin structure). Subdomains 3 and 4 of the structures were superimposed (blue) to highlight the relative movement of subdomains 1 and 2 (magenta or cyan). Using the classical view of actin as a reference (left view), the 4.7° rotation (calculated with the program DynDom, http://www.sys.uea.ac.uk/dyndom/) between the two major domains of actin can be visualized as two perpendicular rotations of ≈3.3°. The center of this rotation approximately coincides with the junctions between domains, consisting of residue Lys-336 and the helix between residues Ile-136 and Gly-146. Comparison of the profilin–actin structures with any other structure of actin, except for the wide-open structure of profilin–β-actin (36), results in a similar motion of the two major domains (see also Movies S2 and S3). This movement appears less dramatic than previously anticipated (36, 37), but it is probably sufficient to explain the stimulation of nucleotide exchange by profilin. (B) Quenching of tryptophan fluorescence on profilin binding (the results of two identical experiments, with different preparations of both actins, are shown). Profilin binds pY53-actin and unphosphorylated actin with similar affinities (K[d] = 0.090 and 0.057 μM, respectively), but the quenching of tryptophan fluorescence is significantly less for profilin–pY53-actin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20672362 G.Hild, B.Bugyi, and M.Nyitrai (2010).
Conformational dynamics of actin: effectors and implications for biological function.
  Cytoskeleton (Hoboken), 67, 609-629.  
20946985 K.Murakami, T.Yasunaga, T.Q.Noguchi, Y.Gomibuchi, K.X.Ngo, T.Q.Uyeda, and T.Wakabayashi (2010).
Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.
  Cell, 143, 275-287.
PDB codes: 3a5l 3a5m 3a5n 3a5o 3g37
20100837 X.Liu, S.Shu, M.S.Hong, B.Yu, and E.D.Korn (2010).
Mutation of actin Tyr-53 alters the conformations of the DNase I-binding loop and the nucleotide-binding cleft.
  J Biol Chem, 285, 9729-9739.  
19289059 R.Kardos, K.Pozsonyi, E.Nevalainen, P.Lappalainen, M.Nyitrai, and G.Hild (2009).
The effects of ADF/cofilin and profilin on the conformation of the ATP-binding cleft of monomeric actin.
  Biophys J, 96, 2335-2343.  
19415654 S.Staubach, H.Razawi, and F.G.Hanisch (2009).
Proteomics of MUC1-containing lipid rafts from plasma membranes and exosomes of human breast carcinoma cells MCF-7.
  Proteomics, 9, 2820-2835.  
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.