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PDBsum entry 1nr0

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protein metals links
Structural protein PDB id
1nr0
Jmol
Contents
Protein chain
610 a.a. *
Metals
_MN
Waters ×709
* Residue conservation analysis
PDB id:
1nr0
Name: Structural protein
Title: Two seven-bladed beta-propeller domains revealed by the structure of a c. Elegans homologue of yeast actin interacting protein 1 (aip1).
Structure: Actin interacting protein 1. Chain: a. Synonym: aip1, uncoordinated protein 78. Engineered: yes
Source: Caenorhabditis elegans. Organism_taxid: 6239. Gene: unc-78 or c04f6.4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.70Å     R-factor:   0.199     R-free:   0.230
Authors: S.M.Vorobiev,K.Mohri,S.Ono,S.C.Almo,S.K.Burley,New York Sgx Research Center For Structural Genomics (Nysgxrc)
Key ref:
K.Mohri et al. (2004). Identification of functional residues on Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing factor/cofilin-bound actin filaments. J Biol Chem, 279, 31697-31707. PubMed id: 15150269 DOI: 10.1074/jbc.M403351200
Date:
23-Jan-03     Release date:   01-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q11176  (WDR1_CAEEL) -  Actin-interacting protein 1
Seq:
Struc:
 
Seq:
Struc:
611 a.a.
610 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     locomotion   6 terms 
  Biochemical function     actin binding     2 terms  

 

 
DOI no: 10.1074/jbc.M403351200 J Biol Chem 279:31697-31707 (2004)
PubMed id: 15150269  
 
 
Identification of functional residues on Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing factor/cofilin-bound actin filaments.
K.Mohri, S.Vorobiev, A.A.Fedorov, S.C.Almo, S.Ono.
 
  ABSTRACT  
 
Actin-interacting protein 1 (AIP1) is a WD40 repeat protein that enhances actin filament disassembly in the presence of actin-depolymerizing factor (ADF)/cofilin. AIP1 also caps the barbed end of ADF/cofilin-bound actin filament. However, the mechanism by which AIP1 interacts with ADF/cofilin and actin is not clearly understood. We determined the crystal structure of Caenorhabditis elegans AIP1 (UNC-78), which revealed 14 WD40 modules arranged in two seven-bladed beta-propeller domains. The structure allowed for the mapping of conserved surface residues, and mutagenesis studies identified five residues that affected the ADF/cofilin-dependent actin filament disassembly activity. Mutations of these residues, which reside in blades 3 and 4 in the N-terminal propeller domain, had significant effects on the disassembly activity but did not alter the barbed end capping activity. These data support a model in which this conserved surface of AIP1 plays a direct role in enhancing fragmentation/depolymerization of ADF/cofilin-bound actin filaments but not in barbed end capping.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Structure of UNC-78. A, ribbon diagram of UNC-78 showing two covalently linked seven-bladed -propellers. The nomenclature used to describe the blades and strands is shown. Middle, view down the axis of the N-terminal -propeller domain; left, side view of UNC-78 showing the concave and convex surfaces. This orientation is obtained by a 90° rotation about the vertical axis relative to the middle image. The arrow identifies the approximate location of the pseudo-2-fold axis (i.e. 167°) that relates the two individual domains Right, view down the axis of the C-terminal -propeller domain. This orientation is obtained by successive rotations of 60 and 20° about the horizontal and vertical axes relative to the middle image. B and C, the hydrogen bonds that are important for the domain/domain interface in UNC-78. B, five selected main chain-main chain hydrogen bonds are marked: Lys9 N-Thr50 O (a), Ile^327 N-Gly599 O (b), Ala^326 O-Ala^344 N (c), Leu13 N-His323 O (d), and Arg15 N-Cys36 O (e). C, side chain-side chain hydrogen bonds between conserved residue His323 of the first domain and Ser341 and Asp343 of the second domain are shown. The side chain of conserved residue Trp351 stabilizes this interaction. D, superposition of the C. elegans (red) and S. cerevisiae (blue) AIP1 (PDB code 1PI6 [PDB] ). The two molecules were superimposed on the basis of the N-terminal -propeller domains, which highlights the 9° greaterclosure between domains in the yeast protein. E, stereo view of the 2F[o] - F[c] electron density map of the WD40 repeat "structural tetrad" formed between Trp563 in strand C, Thr553 in strand B, His535 in the DA loop between two successive repeats, and the conservative Asp557 in the turn between strands B and C. Electron density contours at 1.5 .
Figure 3.
FIG. 3. Conserved surface residues of AIP1. Conserved surface residues of AIP1 that were selected for mutagenesis are shown in red. Green residues are conserved but corresponding to the consensus sequence of WD40 repeats. Blue residues are charged and highly conserved but buried inside the molecule. The structures on the left are views from the top of propellers, and those on the right are from the bottom of propeller 1. The structures are shown in space-filling models (top) and ribbon diagrams (bottom).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 31697-31707) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21468892 C.Xu, and J.Min (2011).
Structure and function of WD40 domain proteins.
  Protein Cell, 2, 202-214.
PDB codes: 3e0c 3fm0 3i2n 3ow8
20668166 C.H.Choi, H.Patel, and D.L.Barber (2010).
Expression of actin-interacting protein 1 suppresses impaired chemotaxis of Dictyostelium cells lacking the Na+-H+ exchanger NHE1.
  Mol Biol Cell, 21, 3162-3170.  
20887964 H.G.Kim, J.W.Ahn, I.Kurth, R.Ullmann, H.T.Kim, A.Kulharya, K.S.Ha, Y.Itokawa, I.Meliciani, W.Wenzel, D.Lee, G.Rosenberger, M.Ozata, D.P.Bick, R.J.Sherins, T.Nagase, M.Tekin, S.H.Kim, C.H.Kim, H.H.Ropers, J.F.Gusella, V.Kalscheuer, C.Y.Choi, and L.C.Layman (2010).
WDR11, a WD protein that interacts with transcription factor EMX1, is mutated in idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.
  Am J Hum Genet, 87, 465-479.  
  20737540 S.Ono (2010).
Dynamic regulation of sarcomeric actin filaments in striated muscle.
  Cytoskeleton (Hoboken), 67, 677-692.  
20631153 Z.L.Chi, F.Yasumoto, Y.Sergeev, M.Minami, M.Obazawa, I.Kimura, Y.Takada, and T.Iwata (2010).
Mutant WDR36 directly affects axon growth of retinal ganglion cells leading to progressive retinal degeneration in mice.
  Hum Mol Genet, 19, 3806-3815.  
19377484 C.K.Lau, J.L.Bachorik, and G.Dreyfuss (2009).
Gemin5-snRNA interaction reveals an RNA binding function for WD repeat domains.
  Nat Struct Mol Biol, 16, 486-491.  
19459188 K.Ono, and S.Ono (2009).
Actin-ADF/cofilin rod formation in Caenorhabditis elegans muscle requires a putative F-actin binding site of ADF/cofilin at the C-terminus.
  Cell Motil Cytoskeleton, 66, 398-408.  
19750007 S.S.Bradrick, and M.Gromeier (2009).
Identification of gemin5 as a novel 7-methylguanosine cap-binding protein.
  PLoS One, 4, e7030.  
19150991 T.K.Footz, J.L.Johnson, S.Dubois, N.Boivin, V.Raymond, and M.A.Walter (2009).
Glaucoma-associated WDR36 variants encode functional defects in a yeast model system.
  Hum Mol Genet, 18, 1276-1287.  
18616971 S.L.Hooper, K.H.Hobbs, and J.B.Thuma (2008).
Invertebrate muscles: thin and thick filament structure; molecular basis of contraction and its regulation, catch and asynchronous muscle.
  Prog Neurobiol, 86, 72.  
17392788 D.A.Hattendorf, A.Andreeva, A.Gangar, P.J.Brennwald, and W.I.Weis (2007).
Structure of the yeast polarity protein Sro7 reveals a SNARE regulatory mechanism.
  Nature, 446, 567-571.
PDB code: 2oaj
17473878 D.Fasshauer, and R.Jahn (2007).
Budding insights on cell polarity.
  Nat Struct Mol Biol, 14, 360-362.  
17293856 J.Li, W.M.Brieher, M.L.Scimone, S.J.Kang, H.Zhu, H.Yin, U.H.von Andrian, T.Mitchison, and J.Yuan (2007).
Caspase-11 regulates cell migration by promoting Aip1-Cofilin-mediated actin depolymerization.
  Nat Cell Biol, 9, 276-286.  
17483419 M.G.Clark, and D.C.Amberg (2007).
Biochemical and genetic analyses provide insight into the structural and mechanistic properties of actin filament disassembly by the Aip1p cofilin complex in Saccharomyces cerevisiae.
  Genetics, 176, 1527-1539.  
17565945 N.Ren, J.Charlton, and P.N.Adler (2007).
The flare gene, which encodes the AIP1 protein of Drosophila, functions to regulate F-actin disassembly in pupal epidermal cells.
  Genetics, 176, 2223-2234.  
17876170 P.Y.Cho, T.I.Kim, S.Li, S.J.Hong, M.H.Choi, S.T.Hong, and Y.E.Chung (2007).
Metacercarial proteins interacting with WD40-repeat protein of Clonorchis sinensis.
  Korean J Parasitol, 45, 229-232.  
17394468 W.Hirschner, H.M.Pogoda, C.Kramer, U.Thiess, B.Hamprecht, K.H.Wiesmüller, M.Lautner, and S.Verleysdonk (2007).
Biosynthesis of Wdr16, a marker protein for kinocilia-bearing cells, starts at the time of kinocilia formation in rat, and wdr16 gene knockdown causes hydrocephalus in zebrafish.
  J Neurochem, 101, 274-288.  
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.  
16525019 K.Mohri, K.Ono, R.Yu, S.Yamashiro, and S.Ono (2006).
Enhancement of actin-depolymerizing factor/cofilin-dependent actin disassembly by actin-interacting protein 1 is required for organized actin filament assembly in the Caenorhabditis elegans body wall muscle.
  Mol Biol Cell, 17, 2190-2199.  
16611742 K.Okada, H.Ravi, E.M.Smith, and B.L.Goode (2006).
Aip1 and cofilin promote rapid turnover of yeast actin patches and cables: a coordinated mechanism for severing and capping filaments.
  Mol Biol Cell, 17, 2855-2868.  
16597697 K.Ono, R.Yu, K.Mohri, and S.Ono (2006).
Caenorhabditis elegans kettin, a large immunoglobulin-like repeat protein, binds to filamentous actin and provides mechanical stability to the contractile apparatuses in body wall muscle.
  Mol Biol Cell, 17, 2722-2734.  
16421248 M.G.Clark, J.Teply, B.K.Haarer, S.C.Viggiano, D.Sept, and D.C.Amberg (2006).
A genetic dissection of Aip1p's interactions leads to a model for Aip1p-cofilin cooperative activities.
  Mol Biol Cell, 17, 1971-1984.  
16937397 R.Yu, and S.Ono (2006).
Dual roles of tropomyosin as an F-actin stabilizer and a regulator of muscle contraction in Caenorhabditis elegans body wall muscle.
  Cell Motil Cytoskeleton, 63, 659-672.  
15581887 I.I.Serysheva, S.L.Hamilton, W.Chiu, and S.J.Ludtke (2005).
Structure of Ca2+ release channel at 14 A resolution.
  J Mol Biol, 345, 427-431.  
15886095 S.Nicholson-Dykstra, H.N.Higgs, and E.S.Harris (2005).
Actin dynamics: growth from dendritic branches.
  Curr Biol, 15, R346-R357.  
16453162 S.Ono, K.Mohri, and K.Ono (2005).
Molecular and biochemical characterization of kettin in Caenorhabditis elegans.
  J Muscle Res Cell Motil, 26, 449-454.  
16245940 S.Yamashiro, K.Mohri, and S.Ono (2005).
The two Caenorhabditis elegans actin-depolymerizing factor/cofilin proteins differently enhance actin filament severing and depolymerization.
  Biochemistry, 44, 14238-14247.  
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.