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PDBsum entry 1kcq

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protein metals links
Structural protein PDB id
1kcq
Jmol
Contents
Protein chain
104 a.a. *
Metals
_CD ×4
Waters ×130
* Residue conservation analysis
PDB id:
1kcq
Name: Structural protein
Title: Human gelsolin domain 2 with a cd2+ bound
Structure: Gelsolin. Chain: a. Fragment: domain 2. Synonym: actin-depolymerizing factor. Brevin. Adf. Agel. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.65Å     R-factor:   0.177     R-free:   0.233
Authors: S.L.Kazmirski,R.L.Isaacson,C.An,A.Buckle,C.M.Johnson,V.Dagge A.R.Fersht
Key ref:
S.L.Kazmirski et al. (2002). Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type. Nat Struct Biol, 9, 112-116. PubMed id: 11753432 DOI: 10.1038/nsb745
Date:
09-Nov-01     Release date:   04-Jan-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06396  (GELS_HUMAN) -  Gelsolin
Seq:
Struc:
 
Seq:
Struc:
782 a.a.
104 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     actin binding     1 term  

 

 
DOI no: 10.1038/nsb745 Nat Struct Biol 9:112-116 (2002)
PubMed id: 11753432  
 
 
Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type.
S.L.Kazmirski, R.L.Isaacson, C.An, A.Buckle, C.M.Johnson, V.Daggett, A.R.Fersht.
 
  ABSTRACT  
 
Mutations in domain 2 (D2, residues 151-266) of the actin-binding protein gelsolin cause familial amyloidosis-Finnish type (FAF). These mutations, D187N or D187Y, lead to abnormal proteolysis of plasma gelsolin at residues 172-173 and a second hydrolysis at residue 243, resulting in an amyloidogenic fragment. Here we present the structure of human gelsolin D2 at 1.65 A and find that Asp 187 is part of a Cd2+ metal-binding site. Two Ca2+ ions are required for a conformational transition of gelsolin to its active form. Differential scanning calorimetry (DSC) and molecular dynamics (MD) simulations suggest that the Cd2+-binding site in D2 is one of these two Ca2+-binding sites and is essential to the stability of D2. Mutation of Asp 187 to Asn disrupts Ca2+ binding in D2, leading to instabilities upon Ca2+ activation. These instabilities make the domain a target for aberrant proteolysis, thereby enacting the first step in the cascade leading to FAF.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The crystal structure of human gelsolin D2 (residues 159 -261 shown). a, The ribbon structure of human gelsolin D2, with the metal-binding site shown. The secondary structure consists of the following residues: 1 is 207 -223; 2, 242 -247; 1, 161 -167; 2, 171 -176; 3, 187 -192; 4, 196 -201; and 5, 230 -235. b, The stereo view of the 2F[o] - F[c] electron density map of gelsolin D2, calculated with SIGMAA coefficients36 and contoured at 1 . The Cd^2+ is coordinated by seven oxygens from four residues and two waters. Asp 187 contributes one carboxyl oxygen to the binding of Cd^2+, whereas the other carboxyl oxygen forms a hydrogen bond with the side chain of Lys 166 (not shown). Mutation of Asp 187 to either Asn or Tyr would knock out the metal-binding capabilities of this site. The refined atomic model is superimposed. The cadmium ion is shown as a gray sphere. Water molecules are labeled as W2 and W3. c, In the structure of Ca^2+-free gelsolin3, Asp 187 forms a salt bridge with Lys 166 (not shown) and Asp 259 points away from the metal-binding site. Mutation of Asp 187 to Asn has been suggested to remove the salt bridge and destabilize the protein3.
Figure 3.
Figure 3. More specific interactions contributing to alterations in structure and dynamics at the aberrant clip site. a, Dynamics of the region surrounding the Ca^2+-binding site and clip site in the simulation of the D187N mutant. Hydrogen bonds are represented by green lines. The distance between the amide hydrogen of Lys 166 and the carbonyl oxygen of Arg 172 is given in magenta. The mutation and clip sites are labeled in red. The C-terminus (C) is Ala 261. Loss of Ca^2+ in the region allows for an increase in the mobility of the C-terminal tail. Salt bridges between the tail region and the turn between -strands 1 and 2 (Glu 258 -Arg 168 and C -Arg 169) are lost as the tail moves away. The consequences of this are (i) the pulling away of -strand 1 from strand 2, resulting from ionic interactions with the C-terminus as it moves away, and (ii) exposure of the region, formerly shielded by the tail, to the solvent. b, Comparison of the human gelsolin D2 and Ca^2+-free, full-length equine gelsolin crystal structures3. In the equine structure (blue), hydrophobic interactions (Leu 211 and Leu 746) and a salt bridge (Arg 207 and Asp 744) hold the C-terminal helix of domain 6 against 1 of D2. c, When the human D2 (gray) is aligned with D2 from the equine Ca^2+-free structure, some differences are observed. The presence of the metal moves 1 away from the C-terminal helix of domain 6 (blue, from the equine structure) and towards the -sheet. This movement disrupts the salt bridge and hydrophobic interactions, facilitating the conformational changes in the C-terminal half of full-length gelsolin. d, The bending in 2 from metal binding would disrupt the hydrogen bonding pattern with the A' strand (between domains 1 and 2). In the equine structure, there are four hydrogen bonds between 2 and the A' strand. e, When the human D2 is aligned with D2 from the equine Ca^2+-free structure, only one of the four hydrogen bonds appears possible. The bending of 2 upon activation of Ca^2+ could induce the breaking off of the A' strand from the -sheet and allow it to form a linker between domain 1 that binds the head of actin and D2 that binds to the side of actin.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 112-116) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21497412 J.L.Fan, X.Z.Wei, L.C.Wan, L.Y.Zhang, X.Q.Zhao, W.Z.Liu, H.Q.Hao, and H.Y.Zhang (2011).
Disarrangement of actin filaments and Ca(2+) gradient by CdCl(2) alters cell wall construction in Arabidopsis thaliana root hairs by inhibiting vesicular trafficking.
  J Plant Physiol, 168, 1157-1167.  
19904968 J.P.Solomon, I.T.Yonemoto, A.N.Murray, J.L.Price, E.T.Powers, W.E.Balch, and J.W.Kelly (2009).
The 8 and 5 kDa fragments of plasma gelsolin form amyloid fibrils by a nucleated polymerization mechanism, while the 68 kDa fragment is not amyloidogenic.
  Biochemistry, 48, 11370-11380.  
19666512 S.Nag, Q.Ma, H.Wang, S.Chumnarnsilpa, W.L.Lee, M.Larsson, B.Kannan, M.Hernandez-Valladares, L.D.Burtnick, and R.C.Robinson (2009).
Ca2+ binding by domain 2 plays a critical role in the activation and stabilization of gelsolin.
  Proc Natl Acad Sci U S A, 106, 13713-13718.
PDB codes: 3ffk 3ffn
18192269 B.F.Shaw, H.L.Lelie, A.Durazo, A.M.Nersissian, G.Xu, P.K.Chan, E.B.Gralla, A.Tiwari, L.J.Hayward, D.R.Borchelt, J.S.Valentine, and J.P.Whitelegge (2008).
Detergent-insoluble aggregates associated with amyotrophic lateral sclerosis in transgenic mice contain primarily full-length, unmodified superoxide dismutase-1.
  J Biol Chem, 283, 8340-8350.  
16644738 B.F.Shaw, A.Durazo, A.M.Nersissian, J.P.Whitelegge, K.F.Faull, and J.S.Valentine (2006).
Local unfolding in a destabilized, pathogenic variant of superoxide dismutase 1 observed with H/D exchange and mass spectrometry.
  J Biol Chem, 281, 18167-18176.  
16258946 N.Chastan, S.Baert-Desurmont, P.Saugier-Veber, G.Dérumeaux, A.Cabot, T.Frébourg, and D.Hannequin (2006).
Cardiac conduction alterations in a French family with amyloidosis of the Finnish type with the p.Asp187Tyr mutation in the GSN gene.
  Muscle Nerve, 33, 113-119.  
16020530 J.A.Rodriguez, B.F.Shaw, A.Durazo, S.H.Sohn, P.A.Doucette, A.M.Nersissian, K.F.Faull, D.K.Eggers, A.Tiwari, L.J.Hayward, and J.S.Valentine (2005).
Destabilization of apoprotein is insufficient to explain Cu,Zn-superoxide dismutase-linked ALS pathogenesis.
  Proc Natl Acad Sci U S A, 102, 10516-10521.  
15466469 C.Karlsson, A.M.Korayem, C.Scherfer, O.Loseva, M.S.Dushay, and U.Theopold (2004).
Proteomic analysis of the Drosophila larval hemolymph clot.
  J Biol Chem, 279, 52033-52041.  
15538717 I.Liepina, P.Janmey, C.Czaplewski, and A.Liwo (2004).
Towards gelsolin amyloid formation.
  Biopolymers, 76, 543-548.  
14701846 I.Sirangelo, C.Malmo, C.Iannuzzi, A.Mezzogiorno, M.R.Bianco, M.Papa, and G.Irace (2004).
Fibrillogenesis and cytotoxic activity of the amyloid-forming apomyoglobin mutant W7FW14F.
  J Biol Chem, 279, 13183-13189.  
15215896 L.D.Burtnick, D.Urosev, E.Irobi, K.Narayan, and R.C.Robinson (2004).
Structure of the N-terminal half of gelsolin bound to actin: roles in severing, apoptosis and FAF.
  EMBO J, 23, 2713-2722.
PDB code: 1rgi
12752443 E.Lagarrigue, S.K.Maciver, A.Fattoum, Y.Benyamin, and C.Roustan (2003).
Co-operation of domain-binding and calcium-binding sites in the activation of gelsolin.
  Eur J Biochem, 270, 2236-2243.  
12660995 H.Benyamini, K.Gunasekaran, H.Wolfson, and R.Nussinov (2003).
Conservation and amyloid formation: a study of the gelsolin-like family.
  Proteins, 51, 266-282.  
14675544 M.E.Huff, W.E.Balch, and J.W.Kelly (2003).
Pathological and functional amyloid formation orchestrated by the secretory pathway.
  Curr Opin Struct Biol, 13, 674-682.  
12374855 F.Chiti, M.Calamai, N.Taddei, M.Stefani, G.Ramponi, and C.M.Dobson (2002).
Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases.
  Proc Natl Acad Sci U S A, 99, 16419-16426.  
12244112 I.Sirangelo, C.Malmo, M.Casillo, A.Mezzogiorno, M.Papa, and G.Irace (2002).
Tryptophanyl substitutions in apomyoglobin determine protein aggregation and amyloid-like fibril formation at physiological pH.
  J Biol Chem, 277, 45887-45891.  
11976724 J.W.Kelly (2002).
Towards an understanding of amyloidogenesis.
  Nat Struct Biol, 9, 323-325.  
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.