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PDBsum entry 1smt

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Metalloregulation PDB id
1smt
Jmol
Contents
Protein chains
98 a.a. *
* Residue conservation analysis
PDB id:
1smt
Name: Metalloregulation
Title: Smtb repressor from synechococcus pcc7942
Structure: Transcriptional repressor smtb. Chain: a, b. Engineered: yes
Source: Synechococcus elongatus. Organism_taxid: 1140. Strain: pcc 7942. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.217     R-free:   0.250
Authors: W.J.Cook,L.M.Hall
Key ref:
W.J.Cook et al. (1998). Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins. J Mol Biol, 275, 337-346. PubMed id: 9466913 DOI: 10.1006/jmbi.1997.1443
Date:
16-Sep-97     Release date:   03-Dec-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P30340  (SMTB_SYNE7) -  Transcriptional repressor SmtB
Seq:
Struc:
122 a.a.
98 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: 10.1006/jmbi.1997.1443 J Mol Biol 275:337-346 (1998)
PubMed id: 9466913  
 
 
Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins.
W.J.Cook, S.R.Kar, K.B.Taylor, L.M.Hall.
 
  ABSTRACT  
 
SmtB from Synechococcus PCC7942 is a trans-acting dimeric repressor that is required for Zn(2+)-responsive expression of the metallothionein SmtA. The structure of SmtB was solved using multiple isomorphous replacement techniques and refined at 2.2 A resolution by simulated annealing to an R-factor of 0.218. SmtB displays the classical helix-turn-helix motif found in many DNA-binding proteins. It has an alpha + beta topology, and the arrangement of the three core helices and the beta hairpin is similar to the HNF-3/fork head, CAP and diphtheria toxin repressor proteins. Although there is no zinc in the crystal structure, analysis of a mercuric acetate derivative suggests a total of four Zn2+ binding sites in the dimer. Two of these putative sites are at the opposite ends of the dimer, while the other two are at the dimer interface and are formed by residues contributed from each monomer. The structure of the dimer is such that simultaneous binding for both recognition helices to DNA would require either a bend in the DNA helix or a conformational change in the dimer. The structure of Synechococcus SmtB is the first in this family of metal-binding DNA repressors.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Putative Zn2+-binding sites in SmtB, based on the Hg2+ sites in a crystal soaked in mercuric acetate. (a) Residues 50 to 64 and 94 to 100 from monomer A. (B) Residues 116 to 121 and 103 to 107 from monomers A (red) and B (green), respectively. The mercury ions are blue. Created with CHAIN (Sack, 1988).
Figure 6.
Figure 6. Model of SmtB binding to DNA, based on the similarity of SmtB with HNF-3/forkhead DNA recognition motif (Clark et al., 1993). The coordinates of SmtB were superimposed onto those of HNF-3, and the actual DNA in HNF-3 was replaced by an idealized B-DNA model. Monomers A and B are green and cyan, respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 275, 337-346) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21077111 A.Schmidt, M.Hagen, E.Schütze, A.Schmidt, and E.Kothe (2010).
In silico prediction of potential metallothioneins and metallohistins in actinobacteria.
  J Basic Microbiol, 50, 562-569.  
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
18454323 A.Bagchi (2009).
Structural characterization of the involvement of SigC in the regulation of the gene expression of pathogenic Mycobacterium ulcerans.
  Mol Biol Rep, 36, 965-969.  
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
19282236 A.O.Summers (2009).
Damage control: regulating defenses against toxic metals and metalloids.
  Curr Opin Microbiol, 12, 138-144.  
19089981 Q.Xu, C.L.Rife, D.Carlton, M.D.Miller, S.S.Krishna, M.A.Elsliger, P.Abdubek, T.Astakhova, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, H.van den Bedem, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.
  Proteins, 74, 1041-1049.
PDB code: 2fna
18591244 E.Ordóñez, S.Thiyagarajan, J.D.Cook, T.L.Stemmler, J.A.Gil, L.M.Mateos, and B.P.Rosen (2008).
Evolution of metal(loid) binding sites in transcriptional regulators.
  J Biol Chem, 283, 25706-25714.  
18076033 H.Itou, M.Yao, N.Watanabe, and I.Tanaka (2008).
Crystal structure of the PH1932 protein, a unique archaeal ArsR type winged-HTH transcription factor from Pyrococcus horikoshii OT3.
  Proteins, 70, 1631-1634.
PDB code: 1uly
18042675 M.C.Reddy, K.Gokulan, W.R.Jacobs, T.R.Ioerger, and J.C.Sacchettini (2008).
Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response.
  Protein Sci, 17, 159-170.
PDB code: 2qz8
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.  
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.  
17322537 E.A.Sieminska, X.Xu, A.Savchenko, and D.A.Sanders (2007).
The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor.
  Protein Sci, 16, 543-549.
PDB code: 2f2e
17897948 J.Qin, H.L.Fu, J.Ye, K.Z.Bencze, T.L.Stemmler, D.E.Rawlings, and B.P.Rosen (2007).
Convergent evolution of a new arsenic binding site in the ArsR/SmtB family of metalloregulators.
  J Biol Chem, 282, 34346-34355.  
17098741 K.Arita, H.Hashimoto, K.Igari, M.Akaboshi, S.Kutsuna, M.Sato, and T.Shimizu (2007).
Structural and biochemical characterization of a cyanobacterium circadian clock-modifier protein.
  J Biol Chem, 282, 1128-1135.
PDB code: 2e1n
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
16751342 A.Kaur, M.Pan, M.Meislin, M.T.Facciotti, R.El-Gewely, and N.S.Baliga (2006).
A systems view of haloarchaeal strategies to withstand stress from transition metals.
  Genome Res, 16, 841-854.  
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.  
17116251 R.P.Saha, and P.Chakrabarti (2006).
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU.
  BMC Struct Biol, 6, 24.  
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
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
16209951 M.Hong, M.Fuangthong, J.D.Helmann, and R.G.Brennan (2005).
Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family.
  Mol Cell, 20, 131-141.
PDB codes: 1z91 1z9c
14960592 R.García-Castellanos, G.Mallorquí-Fernández, A.Marrero, J.Potempa, M.Coll, and F.X.Gomis-Rüth (2004).
On the transcriptional regulation of methicillin resistance: MecI repressor in complex with its operator.
  J Biol Chem, 279, 17888-17896.
PDB code: 1sax
12829272 D.K.Blencowe, and A.P.Morby (2003).
Zn(II) metabolism in prokaryotes.
  FEMS Microbiol Rev, 27, 291-311.  
12939264 J.S.Cavet, A.I.Graham, W.Meng, and N.J.Robinson (2003).
A cadmium-lead-sensing ArsR-SmtB repressor with novel sensory sites. Complementary metal discrimination by NmtR AND CmtR in a common cytosol.
  J Biol Chem, 278, 44560-44566.  
12829266 J.S.Cavet, G.P.Borrelly, and N.J.Robinson (2003).
Zn, Cu and Co in cyanobacteria: selective control of metal availability.
  FEMS Microbiol Rev, 27, 165-181.  
12813082 J.Yu, G.Shen, T.Wang, D.A.Bryant, J.H.Golbeck, and L.McIntosh (2003).
Suppressor mutations in the study of photosystem I biogenesis: sll0088 is a previously unidentified gene involved in reaction center accumulation in Synechocystis sp. strain PCC 6803.
  J Bacteriol, 185, 3878-3887.  
12829264 L.S.Busenlehner, M.A.Pennella, and D.P.Giedroc (2003).
The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance.
  FEMS Microbiol Rev, 27, 131-143.  
12651949 M.A.Pennella, J.E.Shokes, N.J.Cosper, R.A.Scott, and D.P.Giedroc (2003).
Structural elements of metal selectivity in metal sensor proteins.
  Proc Natl Acad Sci U S A, 100, 3713-3718.  
12962631 N.Mizuno, G.Voordouw, K.Miki, A.Sarai, and Y.Higuchi (2003).
Crystal structure of dissimilatory sulfite reductase D (DsrD) protein--possible interaction with B- and Z-DNA by its winged-helix motif.
  Structure, 11, 1133-1140.
PDB code: 1ucr
12881514 R.García-Castellanos, A.Marrero, G.Mallorquí-Fernández, J.Potempa, M.Coll, and F.X.Gomis-Ruth (2003).
Three-dimensional structure of MecI. Molecular basis for transcriptional regulation of staphylococcal methicillin resistance.
  J Biol Chem, 278, 39897-39905.
PDB code: 1okr
14580210 S.A.Lieser, T.C.Davis, J.D.Helmann, and S.M.Cohen (2003).
DNA-binding and oligomerization studies of the manganese(II) metalloregulatory protein MntR from Bacillus subtilis.
  Biochemistry, 42, 12634-12642.  
12829274 S.Silver (2003).
Bacterial silver resistance: molecular biology and uses and misuses of silver compounds.
  FEMS Microbiol Rev, 27, 341-353.  
12399499 B.Barcelona-Andrés, A.Marina, and V.Rubio (2002).
Gene structure, organization, expression, and potential regulatory mechanisms of arginine catabolism in Enterococcus faecalis.
  J Bacteriol, 184, 6289-6300.  
12163508 J.S.Cavet, W.Meng, M.A.Pennella, R.J.Appelhoff, D.P.Giedroc, and N.J.Robinson (2002).
A nickel-cobalt-sensing ArsR-SmtB family repressor. Contributions of cytosol and effector binding sites to metal selectivity.
  J Biol Chem, 277, 38441-38448.  
12176999 M.D.Wong, Y.F.Lin, and B.P.Rosen (2002).
The soft metal ion binding sites in the Staphylococcus aureus pI258 CadC Cd(II)/Pb(II)/Zn(II)-responsive repressor are formed between subunits of the homodimer.
  J Biol Chem, 277, 40930-40936.  
12146942 M.L.VanZile, X.Chen, and D.P.Giedroc (2002).
Structural characterization of distinct alpha3N and alpha5 metal sites in the cyanobacterial zinc sensor SmtB.
  Biochemistry, 41, 9765-9775.  
12146943 M.L.VanZile, X.Chen, and D.P.Giedroc (2002).
Allosteric negative regulation of smt O/P binding of the zinc sensor, SmtB, by metal ions: a coupled equilibrium analysis.
  Biochemistry, 41, 9776-9786.  
12145214 M.Selmer, and X.D.Su (2002).
Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
  EMBO J, 21, 4145-4153.
PDB code: 1lva
11877432 R.G.Zhang, Y.Kim, T.Skarina, S.Beasley, R.Laskowski, C.Arrowsmith, A.Edwards, A.Joachimiak, and A.Savchenko (2002).
Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
  J Biol Chem, 277, 19183-19190.
PDB code: 1mkm
12068812 Y.Sun, M.D.Wong, and B.P.Rosen (2002).
Both metal binding sites in the homodimer are required for metalloregulation by the CadC repressor.
  Mol Microbiol, 44, 1323-1329.  
11248041 K.Kamada, J.De Angelis, R.G.Roeder, and S.K.Burley (2001).
Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF.
  Proc Natl Acad Sci U S A, 98, 3115-3120.
PDB code: 1i27
11171970 K.Yamada, N.Kunishima, K.Mayanagi, T.Ohnishi, T.Nishino, H.Iwasaki, H.Shinagawa, and K.Morikawa (2001).
Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.
  Proc Natl Acad Sci U S A, 98, 1442-1447.
PDB code: 1hqc
11284699 L.S.Busenlehner, N.J.Cosper, R.A.Scott, B.P.Rosen, M.D.Wong, and D.P.Giedroc (2001).
Spectroscopic properties of the metalloregulatory Cd(II) and Pb(II) sites of S. aureus pI258 CadC.
  Biochemistry, 40, 4426-4436.  
10679470 K.S.Gajiwala, and S.K.Burley (2000).
Winged helix proteins.
  Curr Opin Struct Biol, 10, 110-116.  
10692354 M.García-Domínguez, L.Lopez-Maury, F.J.Florencio, and J.C.Reyes (2000).
A gene cluster involved in metal homeostasis in the cyanobacterium Synechocystis sp. strain PCC 6803.
  J Bacteriol, 182, 1507-1514.  
10995250 M.L.VanZile, N.J.Cosper, R.A.Scott, and D.P.Giedroc (2000).
The zinc metalloregulatory protein Synechococcus PCC7942 SmtB binds a single zinc ion per monomer with high affinity in a tetrahedral coordination geometry.
  Biochemistry, 39, 11818-11829.  
10760146 Q.Que, and J.D.Helmann (2000).
Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins.
  Mol Microbiol, 35, 1454-1468.  
10608803 C.E.Outten, F.W.Outten, and T.V.O'Halloran (1999).
DNA distortion mechanism for transcriptional activation by ZntR, a Zn(II)-responsive MerR homologue in Escherichia coli.
  J Biol Chem, 274, 37517-37524.  
10464323 J.C.Rutherford, J.S.Cavet, and N.J.Robinson (1999).
Cobalt-dependent transcriptional switching by a dual-effector MerR-like protein regulates a cobalt-exporting variant CPx-type ATPase.
  J Biol Chem, 274, 25827-25832.  
10411736 V.K.Singh, A.Xiong, T.R.Usgaard, S.Chakrabarti, R.Deora, T.K.Misra, and R.K.Jayaswal (1999).
ZntR is an autoregulatory protein and negatively regulates the chromosomal zinc resistance operon znt of Staphylococcus aureus.
  Mol Microbiol, 33, 200-207.  
  9811636 A.Gaballa, and J.D.Helmann (1998).
Identification of a zinc-specific metalloregulatory protein, Zur, controlling zinc transport operons in Bacillus subtilis.
  J Bacteriol, 180, 5815-5821.  
9724772 C.Thelwell, N.J.Robinson, and J.S.Turner-Cavet (1998).
An SmtB-like repressor from Synechocystis PCC 6803 regulates a zinc exporter.
  Proc Natl Acad Sci U S A, 95, 10728-10733.  
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.