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PDBsum entry 1r23

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protein metals Protein-protein interface(s) links
Transcription repressor PDB id
1r23
Jmol
Contents
Protein chains
104 a.a. *
97 a.a. *
Metals
_ZN
Waters ×123
* Residue conservation analysis
PDB id:
1r23
Name: Transcription repressor
Title: Crystal structure of the cyanobacterial metallothionein repressor smtb in the zn1-form (one zn(ii) per dimer)
Structure: Transcriptional repressor smtb. Chain: a, b. Engineered: yes
Source: Synechococcus elongatus pcc 7942. Organism_taxid: 1140. Strain: pcc7942. Gene: smtb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.204     R-free:   0.236
Authors: C.Eicken,M.A.Pennella,X.Chen,K.M.Koshlap,M.L.Vanzile, J.C.Sacchettini,D.P.Giedroc
Key ref:
C.Eicken et al. (2003). A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins. J Mol Biol, 333, 683-695. PubMed id: 14568530 DOI: 10.1016/j.jmb.2003.09.007
Date:
25-Sep-03     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P30340  (SMTB_SYNE7) -  Transcriptional repressor SmtB
Seq:
Struc:
122 a.a.
104 a.a.
Protein chain
Pfam   ArchSchema ?
P30340  (SMTB_SYNE7) -  Transcriptional repressor SmtB
Seq:
Struc:
122 a.a.
97 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1016/j.jmb.2003.09.007 J Mol Biol 333:683-695 (2003)
PubMed id: 14568530  
 
 
A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins.
C.Eicken, M.A.Pennella, X.Chen, K.M.Koshlap, M.L.VanZile, J.C.Sacchettini, D.P.Giedroc.
 
  ABSTRACT  
 
The origin of metal ion selectivity by members of the SmtB/ArsR family of bacterial metal-sensing transcriptional repressors and the mechanism of negative allosteric regulation of DNA binding is poorly understood. Here, we report that two homologous zinc sensors, Staphylococcus aureus CzrA and cyanobacterial SmtB, are "winged" helix homodimeric DNA-binding proteins that bind Zn(II) to a pair of tetrahedral, interhelical binding sites, with two ligands derived from the alpha5 helix of one subunit, Asp84 O(delta1) (Asp104 in SmtB), His86 N(delta1) (His106), and two derived from the alpha5 helix of the other, His97' N(delta1) (His117') and His100' N(epsilon2) (Glu120'). Formation of the metal chelate drives a quaternary structural switch mediated by an intersubunit hydrogen-binding network that originates with the non-liganding N(epsilon2) face of His97 in CzrA (His117 in SmtB) that stabilizes a low-affinity, DNA-binding conformation. The structure of the Zn(1) SmtB homodimer shows that both metal-binding sites of the dimer must be occupied for the quaternary structural switch to occur. Thus, a critical zinc-ligating histidine residue obligatorily couples formation of the metal-sensing coordination chelate to changes in the conformation and dynamics of the putative DNA-binding helices.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of cyanobacterial SmtB. (a) Sequence alignment of Synechococcus SmtB and S. aureus CzrA, pointing out the location of the proposed ligands to the a3N (red boxes) and a5 (blue boxes) metal-binding sites.[16.] (b) Ribbon representation of the structure of homodimeric apo-SmtB solved to 1.7 Å resolution, with the side-chains of the proposed ligands of one of the a5 metal sites indicated (see (a)). Secondary structural units (N-a1-a2-a3-aR(a4)-b1-b2-a5-C) are indicated for the gold-shaded protomer. In the gold-shaded subunit, C-terminal residues 119-121, including zinc ligand Glu120, are not visible in the electron density maps, indicative of significant disorder in the absence of zinc. (c) Superposition of apo-SmtB (green and gold-colored protomers) with Zn[2] a5-SmtB (blue and cyan-colored subunits), the latter solved to 2.3 Å resolution. The polypeptide chain could not be traced from residues 92-97 in the blue-colored Zn[2] a5-SmtB subunit. The Figure was generated by performing a superposition of the C^a atoms of the a5 helices of the green- and blue-shaded subunits of apo- and Zn[2] a5-SmtB, respectively. This illustrates the large movement of the HTH and b-wings of one subunit relative to the other, represented by a movement of the Ser74 C^a atoms positioned toward the N terminus of the aR helix by 4.8 Å. (d) Superposition of the metal-binding residues in the apo- and Zn[2] forms of SmtB derived from the superposition shown in Figure 1(c). Figures were created using SPOCK: http://mackerel.tamu.edu/spock
Figure 2.
Figure 2. Structure of S. aureus CzrA. (a) Ribbon representation of the structure of apo-CzrA solved to 2.0 Å resolution with all four subunits of the asymmetric unit shown. The secondary structural units for the gold subunit are shown. (b) Global C^a trace subunit-based superposition of apo-CzrA with Zn[2] CzrA, the latter solved to 2.3 Å resolution. (c) Representative structure of the zinc coordination chelate of Zn[2] a5-SmtB superimposed on that derived from Zn[2] CzrA.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 333, 683-695) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20442958 D.Osman, and J.S.Cavet (2010).
Bacterial metal-sensing proteins exemplified by ArsR-SmtB family repressors.
  Nat Prod Rep, 27, 668-680.  
19926656 H.Zhao, A.Volkov, V.H.Veldore, J.A.Hoch, and K.I.Varughese (2010).
Crystal structure of the transcriptional repressor PagR of Bacillus anthracis.
  Microbiology, 156, 385-391.
PDB code: 2zkz
20442957 J.S.Iwig, and P.T.Chivers (2010).
Coordinating intracellular nickel-metal-site structure-function relationships and the NikR and RcnR repressors.
  Nat Prod Rep, 27, 658-667.  
20534443 L.Ni, W.Xu, M.Kumaraswami, and M.A.Schumacher (2010).
Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition.
  Proc Natl Acad Sci U S A, 107, 11763-11768.
PDB codes: 3m89 3m8e 3m8f 3m8k 3m9a
20724137 Y.Kawakami, M.S.Siddiki, K.Inoue, H.Otabayashi, K.Yoshida, S.Ueda, H.Miyasaka, and I.Maeda (2010).
Application of fluorescent protein-tagged trans factors and immobilized cis elements to monitoring of toxic metals based on in vitro protein-DNA interactions.
  Biosens Bioelectron, 26, 1466-1473.  
19822742 A.I.Arunkumar, G.C.Campanello, and D.P.Giedroc (2009).
Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state.
  Proc Natl Acad Sci U S A, 106, 18177-18182.
PDB codes: 2kjb 2kjc
19286656 A.Kandegedara, S.Thiyagarajan, K.C.Kondapalli, T.L.Stemmler, and B.P.Rosen (2009).
Role of Bound Zn(II) in the CadC Cd(II)/Pb(II)/Zn(II)-responsive Repressor.
  J Biol Chem, 284, 14958-14965.
PDB code: 3f72
19995076 N.E.Grossoehme, and D.P.Giedroc (2009).
Energetics of allosteric negative coupling in the zinc sensor S. aureus CzrA.
  J Am Chem Soc, 131, 17860-17870.  
19319388 S.C.Wang, A.V.Dias, and D.B.Zamble (2009).
The "metallo-specific" response of proteins: a perspective based on the Escherichia coli transcriptional regulator NikR.
  Dalton Trans, (), 2459-2466.  
19129220 W.Eiamphungporn, S.Soonsanga, J.W.Lee, and J.D.Helmann (2009).
Oxidation of a single active site suffices for the functional inactivation of the dimeric Bacillus subtilis OhrR repressor in vitro.
  Nucleic Acids Res, 37, 1174-1181.  
19928961 Z.Ma, D.M.Cowart, B.P.Ward, R.J.Arnold, R.D.DiMarchi, L.Zhang, G.N.George, R.A.Scott, and D.P.Giedroc (2009).
Unnatural amino acid substitution as a probe of the allosteric coupling pathway in a mycobacterial Cu(I) sensor.
  J Am Chem Soc, 131, 18044-18045.  
19788177 Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.
  Chem Rev, 109, 4644-4681.  
18042678 J.C.Ebert, and R.B.Altman (2008).
Robust recognition of zinc binding sites in proteins.
  Protein Sci, 17, 54-65.  
18505253 J.S.Iwig, S.Leitch, R.W.Herbst, M.J.Maroney, and P.T.Chivers (2008).
Ni(II) and Co(II) sensing by Escherichia coli RcnR.
  J Am Chem Soc, 130, 7592-7606.  
18795800 T.Liu, X.Chen, Z.Ma, J.Shokes, L.Hemmingsen, R.A.Scott, and D.P.Giedroc (2008).
A Cu(I)-sensing ArsR family metal sensor protein with a relaxed metal selectivity profile.
  Biochemistry, 47, 10564-10575.  
17637984 D.P.Giedroc, and A.I.Arunkumar (2007).
Metal sensor proteins: nature's metalloregulated allosteric switches.
  Dalton Trans, (), 3107-3120.  
17726022 D.R.Campbell, K.E.Chapman, K.J.Waldron, S.Tottey, S.Kendall, G.Cavallaro, C.Andreini, J.Hinds, N.G.Stoker, N.J.Robinson, and J.S.Cavet (2007).
Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent.
  J Biol Chem, 282, 32298-32310.  
17599915 L.Banci, I.Bertini, F.Cantini, S.Ciofi-Baffoni, J.S.Cavet, C.Dennison, A.I.Graham, D.R.Harvie, and N.J.Robinson (2007).
NMR structural analysis of cadmium sensing by winged helix repressor CmtR.
  J Biol Chem, 282, 30181-30188.
PDB code: 2jsc
17109885 T.Kawamura, L.U.Le, H.Zhou, and F.W.Dahlquist (2007).
Solution structure of Escherichia coli PapI, a key regulator of the pap pili phase variation.
  J Mol Biol, 365, 1130-1142.
PDB code: 2htj
16855817 C.V.Romão, E.P.Mitchell, and S.McSweeney (2006).
The crystal structure of Deinococcus radiodurans Dps protein (DR2263) reveals the presence of a novel metal centre in the N terminus.
  J Biol Inorg Chem, 11, 891-902.
PDB codes: 2c2f 2c2u
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.
  Mol Microbiol, 59, 1341-1356.  
  16877320 M.Bose, D.Slick, M.J.Sarto, P.Murphy, D.Roberts, J.Roberts, and R.D.Barber (2006).
Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED).
  Archaea, 2, 39-49.  
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.
  Biochemistry, 45, 15359-15372.  
17116251 R.P.Saha, and P.Chakrabarti (2006).
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU.
  BMC Struct Biol, 6, 24.  
17057345 T.D.Romo, J.C.Sacchettini, and T.R.Ioerger (2006).
Improving amino-acid identification, fit and C(alpha) prediction using the Simplex method in automated model building.
  Acta Crystallogr D Biol Crystallogr, 62, 1401-1406.  
16506234 U.Okada, N.Sakai, M.Yao, N.Watanabe, and I.Tanaka (2006).
Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3.
  Proteins, 63, 1084-1086.
PDB code: 1ub9
15937153 C.Rensing (2005).
Form and function in metal-dependent transcriptional regulation: dawn of the enlightenment.
  J Bacteriol, 187, 3909-3912.  
15937183 J.Ye, A.Kandegedara, P.Martin, and B.P.Rosen (2005).
Crystal structure of the Staphylococcus aureus pI258 CadC Cd(II)/Pb(II)/Zn(II)-responsive repressor.
  J Bacteriol, 187, 4214-4221.
PDB code: 1u2w
16158234 M.A.Pennella, and D.P.Giedroc (2005).
Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulators.
  Biometals, 18, 413-428.  
16133099 S.Silver, and l.e. .T.Phung (2005).
A bacterial view of the periodic table: genes and proteins for toxic inorganic ions.
  J Ind Microbiol Biotechnol, 32, 587-605.  
14960585 T.Liu, S.Nakashima, K.Hirose, M.Shibasaka, M.Katsuhara, B.Ezaki, D.P.Giedroc, and K.Kasamo (2004).
A novel cyanobacterial SmtB/ArsR family repressor regulates the expression of a CPx-ATPase and a metallothionein in response to both Cu(I)/Ag(I) and Zn(II)/Cd(II).
  J Biol Chem, 279, 17810-17818.  
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 code is shown on the right.