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PDBsum entry 1nmd

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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
1nmd
Jmol
Contents
Protein chains
362 a.a.
123 a.a. *
Ligands
SO4
ATP
SO2
Metals
_CA
Waters ×363
* Residue conservation analysis
PDB id:
1nmd
Name: Structural protein
Title: Crystal structure of d. Discoideum actin-gelsolin segment 1 complex crystallized in presence of lithium atp
Structure: Actin. Chain: a. Gelsolin. Chain: g. Fragment: domain i. Synonym: actin-depolymerizing factor, adf, brevin, agel. Engineered: yes
Source: Dictyostelium discoideum. Organism_taxid: 44689. Homo sapiens. Human. Organism_taxid: 9606. Gene: gsn. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.203     R-free:   0.250
Authors: S.M.Vorobiev,S.Welti,J.Condeelis,S.C.Almo
Key ref:
S.Vorobiev et al. (2003). The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism. Proc Natl Acad Sci U S A, 100, 5760-5765. PubMed id: 12732734 DOI: 10.1073/pnas.0832273100
Date:
09-Jan-03     Release date:   04-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07830  (ACT1_DICDI) -  Major actin
Seq:
Struc:
376 a.a.
362 a.a.*
Protein chain
Pfam   ArchSchema ?
P06396  (GELS_HUMAN) -  Gelsolin
Seq:
Struc:
 
Seq:
Struc:
782 a.a.
123 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   10 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1073/pnas.0832273100 Proc Natl Acad Sci U S A 100:5760-5765 (2003)
PubMed id: 12732734  
 
 
The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism.
S.Vorobiev, B.Strokopytov, D.G.Drubin, C.Frieden, S.Ono, J.Condeelis, P.A.Rubenstein, S.C.Almo.
 
  ABSTRACT  
 
The structures of Saccharomyces cerevisiae, Dictyostelium, and Caenorhabditis elegans actin bound to gelsolin segment-1 have been solved and refined at resolutions between 1.9 and 1.75 A. These structures reveal several features relevant to the ATP hydrolytic mechanism, including identification of the nucleophilic water and the roles of Gln-137 and His-161 in positioning and activating the catalytic water, respectively. The involvement of these residues in the catalytic mechanism is consistent with yeast genetics studies. This work highlights both structural and mechanistic similarities with the small and trimeric G proteins and restricts the types of mechanisms responsible for the considerable enhancement of ATP hydrolysis associated with actin polymerization. The conservation of functionalities involved in nucleotide binding and catalysis also provide insights into the mechanistic features of members of the family of actin-related proteins.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overall structure of the yeast actin/gelsolin segment-1 complex. Gelsolin (purple) binds to subdomains 1 and 3 of actin (yellow). Sixteen water molecules (aqua) contribute to the actin-gelsolin binding interface. Eight water molecules (red) form a network across the actin nucleotide binding cleft, contacting residues in subdomains 1, 3, and 4 (red backbone). The gelsolin-associated Ca^2+ ion is represented as pink. The adenine nucleotide is also shown, with the Mg2+ ion in black.
Figure 2.
Fig. 2. Details of the water-mediated hydrogen bonding network across the nucleotide-binding cleft. Eight solvent molecules (black) run across the nucleotide binding cleft and may play a role in transducing changes in the nucleotide state into structural and dynamic changes relevant to polymerization and interactions with regulatory proteins.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19931282 J.Pfaendtner, E.Lyman, T.D.Pollard, and G.A.Voth (2010).
Structure and dynamics of the actin filament.
  J Mol Biol, 396, 252-263.  
20844556 J.Salje, P.Gayathri, and J.Löwe (2010).
The ParMRC system: molecular mechanisms of plasmid segregation by actin-like filaments.
  Nat Rev Microbiol, 8, 683-692.  
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
20215471 S.Viggiano, B.Haarer, and D.C.Amberg (2010).
Correction/completion of the yeast actin, alanine scan alleles.
  Genetics, 185, 391-394.  
19419963 K.E.Bryan, and P.A.Rubenstein (2009).
Allele-specific effects of human deafness gamma-actin mutations (DFNA20/26) on the actin/cofilin interaction.
  J Biol Chem, 284, 18260-18269.  
19477959 M.Morín, K.E.Bryan, F.Mayo-Merino, R.Goodyear, A.Mencía, S.Modamio-Høybjør, I.del Castillo, J.M.Cabalka, G.Richardson, F.Moreno, P.A.Rubenstein, and M.A.Moreno-Pelayo (2009).
In vivo and in vitro effects of two novel gamma-actin (ACTG1) mutations that cause DFNA20/26 hearing impairment.
  Hum Mol Genet, 18, 3075-3089.  
19158791 T.Oda, M.Iwasa, T.Aihara, Y.Maéda, and A.Narita (2009).
The nature of the globular- to fibrous-actin transition.
  Nature, 457, 441-445.
PDB code: 2zwh
18258262 E.E.Grintsevich, S.A.Benchaar, D.Warshaviak, P.Boontheung, F.Halgand, J.P.Whitelegge, K.F.Faull, R.R.Loo, D.Sept, J.A.Loo, and E.Reisler (2008).
Mapping the cofilin binding site on yeast G-actin by chemical cross-linking.
  J Mol Biol, 377, 395-409.  
18689676 K.Baek, X.Liu, F.Ferron, S.Shu, E.D.Korn, and R.Dominguez (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.
PDB codes: 3chw 3ci5 3cip
18391412 M.R.Sawaya, D.S.Kudryashov, I.Pashkov, H.Adisetiyo, E.Reisler, and T.O.Yeates (2008).
Multiple crystal structures of actin dimers and their implications for interactions in the actin filament.
  Acta Crystallogr D Biol Crystallogr, 64, 454-465.
PDB codes: 2q1n 2q31 2q36
18938176 U.B.Nair, P.B.Joel, Q.Wan, S.Lowey, M.A.Rould, and K.M.Trybus (2008).
Crystal structures of monomeric actin bound to cytochalasin D.
  J Mol Biol, 384, 848-864.
PDB codes: 3eks 3eku 3el2
17499050 B.J.Nolen, and T.D.Pollard (2007).
Insights into the influence of nucleotides on actin family proteins from seven structures of Arp2/3 complex.
  Mol Cell, 26, 449-457.
PDB codes: 2p9i 2p9k 2p9l 2p9n 2p9p 2p9s 2p9u
17477841 T.D.Pollard (2007).
Regulation of actin filament assembly by Arp2/3 complex and formins.
  Annu Rev Biophys Biomol Struct, 36, 451-477.  
16862144 A.C.Martin, M.D.Welch, and D.G.Drubin (2006).
Arp2/3 ATP hydrolysis-catalysed branch dissociation is critical for endocytic force generation.
  Nat Cell Biol, 8, 826-833.  
16407404 J.H.Willis, E.Munro, R.Lyczak, and B.Bowerman (2006).
Conditional dominant mutations in the Caenorhabditis elegans gene act-2 identify cytoplasmic and muscle roles for a redundant actin isoform.
  Mol Biol Cell, 17, 1051-1064.  
16428279 T.J.Minehardt, P.A.Kollman, R.Cooke, and E.Pate (2006).
The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin.
  Biophys J, 90, 2445-2449.  
16326908 V.F.Waingeh, C.D.Gustafson, E.I.Kozliak, S.L.Lowe, H.R.Knull, and K.A.Thomasson (2006).
Glycolytic enzyme interactions with yeast and skeletal muscle F-actin.
  Biophys J, 90, 1371-1384.  
16685646 V.Procaccio, G.Salazar, S.Ono, M.L.Styers, M.Gearing, A.Davila, R.Jimenez, J.Juncos, C.A.Gutekunst, G.Meroni, B.Fontanella, E.Sontag, J.M.Sontag, V.Faundez, and B.H.Wainer (2006).
A mutation of beta -actin that alters depolymerization dynamics is associated with autosomal dominant developmental malformations, deafness, and dystonia.
  Am J Hum Genet, 78, 947-960.  
16326906 W.Chen, K.K.Wen, A.E.Sens, and P.A.Rubenstein (2006).
Differential interaction of cardiac, skeletal muscle, and yeast tropomyosins with fluorescent (pyrene235) yeast actin.
  Biophys J, 90, 1308-1318.  
16959967 Y.L.Shih, and L.Rothfield (2006).
The bacterial cytoskeleton.
  Microbiol Mol Biol Rev, 70, 729-754.  
15657399 A.C.Martin, X.P.Xu, I.Rouiller, M.Kaksonen, Y.Sun, L.Belmont, N.Volkmann, D.Hanein, M.Welch, and D.G.Drubin (2005).
Effects of Arp2 and Arp3 nucleotide-binding pocket mutations on Arp2/3 complex function.
  J Cell Biol, 168, 315-328.  
16141336 D.S.Kudryashov, M.R.Sawaya, H.Adisetiyo, T.Norcross, G.Hegyi, E.Reisler, and T.O.Yeates (2005).
The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin.
  Proc Natl Acad Sci U S A, 102, 13105-13110.
PDB code: 2a5x
16195354 J.Muller, Y.Oma, L.Vallar, E.Friederich, O.Poch, and B.Winsor (2005).
Sequence and comparative genomic analysis of actin-related proteins.
  Mol Biol Cell, 16, 5736-5748.  
15505213 B.J.Nolen, R.S.Littlefield, and T.D.Pollard (2004).
Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP.
  Proc Natl Acad Sci U S A, 101, 15627-15632.
PDB codes: 1tyq 1u2v
15540116 O.Drory, F.Frolow, and N.Nelson (2004).
Crystal structure of yeast V-ATPase subunit C reveals its stator function.
  EMBO Rep, 5, 1148-1152.
PDB code: 1u7l
14507709 D.S.Kudryashov, and E.Reisler (2003).
Solution properties of tetramethylrhodamine-modified G-actin.
  Biophys J, 85, 2466-2475.  
14684684 E.van Wijk, E.Krieger, M.H.Kemperman, E.M.De Leenheer, P.L.Huygen, C.W.Cremers, F.P.Cremers, and H.Kremer (2003).
A mutation in the gamma actin 1 (ACTG1) gene causes autosomal dominant hearing loss (DFNA20/26).
  J Med Genet, 40, 879-884.  
14556630 J.Q.Guan, S.C.Almo, E.Reisler, and M.R.Chance (2003).
Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent.
  Biochemistry, 42, 11992-12000.  
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.