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PDBsum entry 2jgo
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protein ligands metals Protein-protein interface(s) links
De novo protein PDB id
2jgo

 

 

 

 

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Contents
Protein chains
31 a.a.
Ligands
ARS
Metals
_ZN ×4
Waters ×53
PDB id:
2jgo
Name: De novo protein
Title: Structure of the arsenated de novo designed peptide coil ser l9c
Structure: Coil ser l9c. Chain: a, b, c. Engineered: yes
Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630
Resolution:
1.81Å     R-factor:   0.201     R-free:   0.257
Authors: D.S.Touw,C.E.Nordman,J.A.Stuckey,V.L.Pecoraro
Key ref:
D.S.Touw et al. (2007). Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils. Proc Natl Acad Sci U S A, 104, 11969-11974. PubMed id: 17609383 DOI: 10.1073/pnas.0701979104
Date:
13-Feb-07     Release date:   10-Jul-07    
PROCHECK
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 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 30 a.a.
Key:    Secondary structure

 

 
DOI no: 10.1073/pnas.0701979104 Proc Natl Acad Sci U S A 104:11969-11974 (2007)
PubMed id: 17609383  
 
 
Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils.
D.S.Touw, C.E.Nordman, J.A.Stuckey, V.L.Pecoraro.
 
  ABSTRACT  
 
Arsenic, a contaminant of water supplies worldwide, is one of the most toxic inorganic ions. Despite arsenic's health impact, there is relatively little structural detail known about its interactions with proteins. Bacteria such as Escherichia coli have evolved arsenic resistance using the Ars operon that is regulated by ArsR, a repressor protein that dissociates from DNA when As(III) binds. This protein undergoes a critical conformational change upon binding As(III) with three cysteine residues. Unfortunately, structures of ArsR with or without As(III) have not been reported. Alternatively, de novo designed peptides can bind As(III) in an endo configuration within a thiolate-rich environment consistent with that proposed for both ArsR and ArsD. We report the structure of the As(III) complex of Coil Ser L9C to a 1.8-A resolution, providing x-ray characterization of As(III) in a Tris thiolate protein environment and allowing a structural basis by which to understand arsenated ArsR.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. The zinc-mediated packing of the coiled coils with Zn(II) and As(III) ions is shown in pink and cyan, respectively. (A) Bottom-up view of a central coiled coil (green) with the six Zn(II) ions that are coordinated by side chains at the C-terminal end. (B) Side view of the trimeric structure of As(CSL9C)[3] with a different perspective of the Zn(II) coordination to the exterior residues of the coiled coils. In both panels, only two of eight symmetry related Zn(II) ions are included for clarity. 		Figure 5.
Fig. 5. The overlay of Coil V[a]L[d], shown in green (PDB entry 1COI), a related parallel three-stranded coiled coil with As(CSL9C)[3] (red) demonstrates their structural similarity and highlights their divergence at the C and N termini where the Zn(II) ions hold CSL9C in a more helical conformation than V[a]L[d].
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22948927 S.S.Cha, Y.J.An, C.S.Jeong, M.K.Kim, S.G.Lee, K.H.Lee, and B.H.Oh (2012).
Experimental phasing using zinc anomalous scattering.
  Acta Crystallogr D Biol Crystallogr, 68, 1253-1258.
PDB codes: 4dt3 4dwz 4fc5
20582349 N.R.Lindquist, T.G.Carter, V.M.Cangelosi, L.N.Zakharov, and D.W.Johnson (2010).
Three's company: co-crystallization of a self-assembled S(4) metallacyclophane with two diastereomeric metallacycle intermediates.
  Chem Commun (Camb), 46, 3505-3507.  
  19579245 A.F.Peacock, J.A.Stuckey, and V.L.Pecoraro (2009).
Switching the chirality of the metal environment alters the coordination mode in designed peptides.
  Angew Chem Int Ed Engl, 48, 7371-7374.
PDB codes: 3h5f 3h5g
19290357 A.F.Peacock, O.Iranzo, and V.L.Pecoraro (2009).
Harnessing natures ability to control metal ion coordination geometry using de novo designed peptides.
  Dalton Trans, (), 2271-2280.  
19637261 A.N.Zaykov, K.R.MacKenzie, and Z.T.Ball (2009).
Controlling peptide structure with coordination chemistry: robust and reversible peptide-dirhodium ligation.
  Chemistry, 15, 8961-8965.  
19282236 A.O.Summers (2009).
Damage control: regulating defenses against toxic metals and metalloids.
  Curr Opin Microbiol, 12, 138-144.  
19102631 D.Ramadan, P.C.Rancy, R.P.Nagarkar, J.P.Schneider, and C.Thorpe (2009).
Arsenic(III) species inhibit oxidative protein folding in vitro.
  Biochemistry, 48, 424-432.  
19229934 O.Iranzo, T.Jakusch, K.H.Lee, L.Hemmingsen, and V.L.Pecoraro (2009).
The correlation of 113Cd NMR and 111mCd PAC spectroscopies provides a powerful approach for the characterization of the structure of Cd(II)-substituted Zn(II) proteins.
  Chemistry, 15, 3761-3772.  
19675646 Y.Lu, N.Yeung, N.Sieracki, and N.M.Marshall (2009).
Design of functional metalloproteins.
  Nature, 460, 855-862.  
18940928 A.F.Peacock, L.Hemmingsen, and V.L.Pecoraro (2008).
Using diastereopeptides to control metal ion coordination in proteins.
  Proc Natl Acad Sci U S A, 105, 16566-16571.  
18959366 M.Łuczkowski, M.Stachura, V.Schirf, B.Demeler, L.Hemmingsen, and V.L.Pecoraro (2008).
Design of thiolate rich metal binding sites within a peptidic framework.
  Inorg Chem, 47, 10875-10888.  
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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