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PDBsum entry 1q06

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protein metals Protein-protein interface(s) links
Transcription PDB id
1q06
Jmol
Contents
Protein chains
122 a.a. *
126 a.a. *
Metals
_AG ×2
Waters ×135
* Residue conservation analysis
PDB id:
1q06
Name: Transcription
Title: Crystal structure of the ag(i) form of e. Coli cuer, a copper efflux regulator
Structure: Transcriptional regulator cuer. Chain: a, b. Synonym: copper efflux regulator, copper export regulator. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: cuer. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.07Å     R-factor:   0.219     R-free:   0.259
Authors: A.Changela,K.Chen,Y.Xue,J.Holschen,C.E.Outten, T.V.O'Halloran,A.Mondragon
Key ref:
A.Changela et al. (2003). Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR. Science, 301, 1383-1387. PubMed id: 12958362 DOI: 10.1126/science.1085950
Date:
15-Jul-03     Release date:   16-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A9G4  (CUER_ECOLI) -  HTH-type transcriptional regulator CueR
Seq:
Struc:
135 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P0A9G4  (CUER_ECOLI) -  HTH-type transcriptional regulator CueR
Seq:
Struc:
135 a.a.
126 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription, DNA-dependent   3 terms 
  Biochemical function     DNA binding     4 terms  

 

 
DOI no: 10.1126/science.1085950 Science 301:1383-1387 (2003)
PubMed id: 12958362  
 
 
Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR.
A.Changela, K.Chen, Y.Xue, J.Holschen, C.E.Outten, T.V.O'Halloran, A.Mondragón.
 
  ABSTRACT  
 
The earliest of a series of copper efflux genes in Escherichia coli are controlled by CueR, a member of the MerR family of transcriptional activators. Thermodynamic calibration of CueR reveals a zeptomolar (10(-21) molar) sensitivity to free Cu+, which is far less than one atom per cell. Atomic details of this extraordinary sensitivity and selectivity for +1transition-metal ions are revealed by comparing the crystal structures of CueR and a Zn2+-sensing homolog, ZntR. An unusual buried metal-receptor site in CueR restricts the metal to a linear, two-coordinate geometry and uses helix-dipole and hydrogen-bonding interactions to enhance metal binding. This binding mode is rare among metalloproteins but well suited for an ultrasensitive genetic switch.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. (A) Overall structure of the Cu-CueR dimer. The ribbon diagram depicts one monomer in gray and the functional domains in the other monomer in color, with the DNA-binding domain in blue, the dimerization helix in red, and the metal-binding domain in purple. The N-terminal DNA-binding domain consists of two helix-turn-helix motifs and a three-stranded antiparallel ß sheet. The second helix-turn-helix motif of the DNA-binding domain is followed by a five-residue loop connecting to a 10-turn helix. This long helix links the DNA-binding domain to the metal-binding domain and contributes to the bulk of the dimerization interface by forming an antiparallel coiled coil with the equivalent helix of the other monomer. The copper ions are shown as cyan spheres, and the coordinating cysteines, Cys112 and Cys120, are highlighted in ball-and-stick representation. Most of the metal-binding loop of one monomer (residues 115 to 119) and the last eight residues at the C-termini of both monomers are disordered and are not included in the model. (B) A space-filling model of CueR reveals the solvent inaccessibility of the bound metal. The protein is shown in gray and its orientation is similar to that used in (A). The sulfur atoms of the cysteine ligands are colored yellow, and the buried Cu+ ion is depicted in blue.
Figure 3.
Fig. 3. (A) Side-by-side close-up views showing details of the metal-binding regions in CueR and ZntR. The CueR structure reveals a linear Cu+ dithiolate coordination by conserved Cys112 and Cys120. The Cu+ ion is depicted as a cyan sphere, and secondary structural elements are shown in the same color scheme as in Fig. 2A. Other functional groups residing on the metal-binding loop are shown, but do not make any contacts to the metal. Ser77 from the other monomer is oriented away from the metal. A close-up view of the metal-binding region of ZntR is presented in a similar orientation to that of CueR. The domains are shown in the same color scheme used for CueR. The two Zn2^+ ions are depicted as green spheres. Zn1 is coordinated to Cys114 and Cys124 of the metal-binding loop, and to Cys79 from the other monomer. Zn2 is coordinated to Cys115 and His119 of the metal-binding loop and Cys79 of the other monomer. Each Zn2^+ atom is also coordinated by an oxygen atom of a bridging phosphate ion, shown in ball-and-stick representation with the phosphate atom colored magenta. The coordinate-covalent bonds to the metal ions are shown in orange. (B) Schematic diagram detailing various hydrogen-bonding interactions at the CueR metal-binding site. Residues from the metal-binding loop and the first turn of the C-terminal helix are shown in black, and residues from the other monomer are highlighted in red. Hydrogen-bonding interactions (within 3.2 Å for N/O donor/acceptor pairs and 3.8 Å for S-X acceptors) are depicted by dotted lines. S-Cu bonds are shown by bold lines. (C) Close-up view looking down along the helix extending from the C-terminus of the metal-binding loop reveals that Cys120 is centered on the helix and only 2.0 Å away from its N-terminus. Whereas Cys112 and the metal ion also appear to be oriented over the helix dipole, both are distant from the N-terminal end of the helix (approximate distances of Cys112 and the Cu+ ion to the N-terminal end of the helix are 6.5 and 4.0 Å, respectively). Structural elements and bonds are colored using the same scheme as in Fig. 2A, and the metal-binding loop has been omitted for clarity.
 
  The above figures are reprinted by permission from the AAAs: Science (2003, 301, 1383-1387) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 3k07 3kso 3kss
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PDB codes: 2ofg 2ofh
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PDB code: 3iao
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PDB codes: 3h94 3h9i 3h9t 3ooc 3opo 3ow7
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19168618 E.L.Benanti, and P.T.Chivers (2009).
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Selective recognition of metal ions by metalloregulatory proteins.
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Protein-folding location can regulate manganese-binding versus copper- or zinc-binding.
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PDB code: 2vqa
18334645 S.Watanabe, A.Kita, K.Kobayashi, and K.Miki (2008).
Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA.
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PDB codes: 2zhg 2zhh
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A Cu(I)-sensing ArsR family metal sensor protein with a relaxed metal selectivity profile.
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Non-heme iron through the three domains of life.
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Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor.
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PDB code: 2jml
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Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X-ray absorption spectroscopy.
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PDB code: 2qcp
17302809 J.L.Hobman (2007).
MerR family transcription activators: similar designs, different specificities.
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17219055 J.M.Argüello, E.Eren, and M.González-Guerrero (2007).
The structure and function of heavy metal transport P1B-ATPases.
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17085574 L.V.Wray, and S.H.Fisher (2007).
Functional analysis of the carboxy-terminal region of Bacillus subtilis TnrA, a MerR family protein.
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17220226 M.Pruteanu, S.B.Neher, and T.A.Baker (2007).
Ligand-controlled proteolysis of the Escherichia coli transcriptional regulator ZntR.
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A more discerning zinc exporter.
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17307845 P.T.Chivers (2007).
A galvanizing story--protein stability and zinc homeostasis.
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Bacterial sensing of and resistance to gold salts.
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Engineered holliday junctions as single-molecule reporters for protein-DNA interactions with application to a MerR-family regulator.
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CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator.
  Nat Chem Biol, 3, 60-68.
PDB code: 2hh7
16526091 C.C.Kung, W.N.Huang, Y.C.Huang, and K.C.Yeh (2006).
Proteomic survey of copper-binding proteins in Arabidopsis roots by immobilized metal affinity chromatography and mass spectrometry.
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16430705 D.R.Harvie, C.Andreini, G.Cavallaro, W.Meng, B.A.Connolly, K.Yoshida, Y.Fujita, C.R.Harwood, D.S.Radford, S.Tottey, J.S.Cavet, and N.J.Robinson (2006).
Predicting metals sensed by ArsR-SmtB repressors: allosteric interference by a non-effector metal.
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Comparative genomics of regulation of heavy metal resistance in Eubacteria.
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16541427 J.F.Fuchs, H.Nedev, D.Poger, M.Ferrand, V.Brenner, J.P.Dognon, and S.Crouzy (2006).
New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics.
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Structural basis for the metal-selective activation of the manganese transport regulator of Bacillus subtilis.
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PDB codes: 2ev0 2ev5 2ev6 2f5c 2f5d 2f5e 2f5f
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16026976 J.P.Sumner, N.M.Westerberg, A.K.Stoddard, T.K.Hurst, M.Cramer, R.B.Thompson, C.A.Fierke, and R.Kopelman (2006).
DsRed as a highly sensitive, selective, and reversible fluorescence-based biosensor for both Cu(+) and Cu(2+) ions.
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The delivery of copper for thylakoid import observed by NMR.
  Proc Natl Acad Sci U S A, 103, 8320-8325.
PDB code: 2gcf
17176058 M.V.Golynskiy, W.A.Gunderson, M.P.Hendrich, and S.M.Cohen (2006).
Metal binding studies and EPR spectroscopy of the manganese transport regulator MntR.
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CopY-like copper inducible repressors are putative 'winged helix' proteins.
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Crystallization and preliminary X-ray crystallographic studies of the oxidative-stress sensor SoxR and its complex with DNA.
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Activation of superoxide dismutases: putting the metal to the pedal.
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The bldC developmental locus of Streptomyces coelicolor encodes a member of a family of small DNA-binding proteins related to the DNA-binding domains of the MerR family.
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15951376 A.Giorgetti, P.Carloni, P.Mistrik, and V.Torre (2005).
A homology model of the pore region of HCN channels.
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Constitutive soxR mutations contribute to multiple-antibiotic resistance in clinical Escherichia coli isolates.
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15948947 C.M.Moore, A.Gaballa, M.Hui, R.W.Ye, and J.D.Helmann (2005).
Genetic and physiological responses of Bacillus subtilis to metal ion stress.
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15802251 C.M.Moore, and J.D.Helmann (2005).
Metal ion homeostasis in Bacillus subtilis.
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16158235 J.L.Hobman, J.Wilkie, and N.L.Brown (2005).
A design for life: prokaryotic metal-binding MerR family regulators.
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15773991 K.Yamamoto, and A.Ishihama (2005).
Transcriptional response of Escherichia coli to external copper.
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One-component systems dominate signal transduction in prokaryotes.
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16158234 M.A.Pennella, and D.P.Giedroc (2005).
Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulators.
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15774872 M.Egler, C.Grosse, G.Grass, and D.H.Nies (2005).
Role of the extracytoplasmic function protein family sigma factor RpoE in metal resistance of Escherichia coli.
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15954738 N.Verma, and M.Singh (2005).
Biosensors for heavy metals.
  Biometals, 18, 121-129.  
15225316 G.P.Borrelly, S.A.Rondet, S.Tottey, and N.J.Robinson (2004).
Chimeras of P-type ATPases and their transcriptional regulators: contributions of a cytosolic amino-terminal domain to metal specificity.
  Mol Microbiol, 53, 217-227.  
14996817 L.Song, J.Caguiat, Z.Li, J.Shokes, R.A.Scott, L.Olliff, and A.O.Summers (2004).
Engineered single-chain, antiparallel, coiled coil mimics the MerR metal binding site.
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15181151 N.Shomron, M.Reznik, and G.Ast (2004).
Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus.
  Mol Biol Cell, 15, 3782-3795.  
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