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PDBsum entry 1b9m
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protein metals Protein-protein interface(s) links
Transcription PDB id
1b9m

 

 

 

 

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Contents
Protein chains
258 a.a. *
Metals
_NI
Waters ×426
* Residue conservation analysis
PDB id:
1b9m
Name: Transcription
Title: Regulator from escherichia coli
Structure: Protein (mode). Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.75Å     R-factor:   0.234     R-free:   0.279
Authors: D.R.Hall,D.G.Gourley,W.N.Hunter
Key ref:
D.R.Hall et al. (1999). The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds. EMBO J, 18, 1435-1446. PubMed id: 10075916 DOI: 10.1093/emboj/18.6.1435
Date:
12-Feb-99     Release date:   15-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P0A9G8  (MODE_ECOLI) -  DNA-binding transcriptional dual regulator ModE from Escherichia coli (strain K12)
Seq:
Struc: 		262 a.a.
258 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1093/emboj/18.6.1435 EMBO J 18:1435-1446 (1999)
PubMed id: 10075916  
 
 
The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds.
D.R.Hall, D.G.Gourley, G.A.Leonard, E.M.Duke, L.A.Anderson, D.H.Boxer, W.N.Hunter.
 
  ABSTRACT  
 
The molybdate-dependent transcriptional regulator (ModE) from Escherichia coli functions as a sensor of molybdate concentration and a regulator for transcription of operons involved in the uptake and utilization of the essential element, molybdenum. We have determined the structure of ModE using multi-wavelength anomalous dispersion. Selenomethionyl and native ModE models are refined to 1. 75 and 2.1 A, respectively and describe the architecture and structural detail of a complete transcriptional regulator. ModE is a homodimer and each subunit comprises N- and C-terminal domains. The N-terminal domain carries a winged helix-turn-helix motif for binding to DNA and is primarily responsible for ModE dimerization. The C-terminal domain contains the molybdate-binding site and residues implicated in binding the oxyanion are identified. This domain is divided into sub-domains a and b which have similar folds, although the organization of secondary structure elements varies. The sub-domain fold is related to the oligomer binding-fold and similar to that of the subunits of several toxins which are involved in extensive protein-protein interactions. This suggests a role for the C-terminal domain in the formation of the ModE-protein-DNA complexes necessary to regulate transcription. Modelling of ModE interacting with DNA suggests that a large distortion of DNA is not necessary for complex formation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Ribbon diagrams to depict the architecture of ModE. (A) Domains I and II. The helices of the HTH motif of domain I are coloured green. Sub-domains a and b of domain II are coloured blue and yellow. Residues Arg128, Lys183 and Trp186 are shown as sticks. (B) A ModE monomer. (C) The dimer with elements of secondary structure at the C-terminal domain assigned to aid orientation of this domain with respect to (A). Figures 2, 3, 4, 5 and 6 were generated with MOLSCRIPT (Kraulis, 1991) and RASTER3D (Merritt and Murphy, 1994). (D) The amino acid sequence with elements of secondary structure that have been assigned. 		Figure 6.
Figure 6 A model of ModE interacting with double helix DNA. The DNA strands are purple and cyan, the palindromic DNA recognition site is black.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 1435-1446) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
20600129 A.Dawson, M.Chen, P.K.Fyfe, Z.Guo, and W.N.Hunter (2010).
Structure and reactivity of Bacillus subtilis MenD catalyzing the first committed step in menaquinone biosynthesis.
  J Mol Biol, 401, 253-264.
PDB code: 2x7j
20230832 M.Kumaraswami, K.J.Newberry, and R.G.Brennan (2010).
Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR.
  J Mol Biol, 398, 264-275.
PDB code: 3iao
19894045 T.Nishitani, M.Shimada, K.Kuroda, and M.Ueda (2010).
Molecular design of yeast cell surface for adsorption and recovery of molybdenum, one of rare metals.
  Appl Microbiol Biotechnol, 86, 641-648.  
19608746 E.M.Warren, H.Huang, E.Fanning, W.J.Chazin, and B.F.Eichman (2009).
Physical interactions between Mcm10, DNA, and DNA polymerase alpha.
  J Biol Chem, 284, 24662-24672.
PDB code: 3h15
19772354 J.A.Hernandez, S.J.George, and L.M.Rubio (2009).
Molybdenum trafficking for nitrogen fixation.
  Biochemistry, 48, 9711-9721.  
19502397 J.Wiethaus, A.Müller, M.Neumann, S.Neumann, S.Leimkühler, F.Narberhaus, and B.Masepohl (2009).
Specific interactions between four molybdenum-binding proteins contribute to Mo-dependent gene regulation in Rhodobacter capsulatus.
  J Bacteriol, 191, 5205-5215.  
19919002 M.E.Taveirne, M.L.Sikes, and J.W.Olson (2009).
Molybdenum and tungsten in Campylobacter jejuni: their physiological role and identification of separate transporters regulated by a single ModE-like protein.
  Mol Microbiol, 74, 758-771.  
18511655 S.Gerber, M.Comellas-Bigler, B.A.Goetz, and K.P.Locher (2008).
Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter.
  Science, 321, 246-250.
PDB code: 3d31
18192278 Y.Shimoda, S.Shinpo, M.Kohara, Y.Nakamura, S.Tabata, and S.Sato (2008).
A large scale analysis of protein-protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti.
  DNA Res, 15, 13-23.  
18485362 Y.Zhang, and V.N.Gladyshev (2008).
Molybdoproteomes and evolution of molybdenum utilization.
  J Mol Biol, 379, 881-899.  
17148509 R.Thilakaraj, K.Raghunathan, S.Anishetty, and G.Pennathur (2007).
In silico identification of putative metal binding motifs.
  Bioinformatics, 23, 267-271.  
17764951 S.J.Lee, A.Böhm, M.Krug, and W.Boos (2007).
The ABC of binding-protein-dependent transport in Archaea.
  Trends Microbiol, 15, 389-397.  
16436801 I.Uchiyama (2006).
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes.
  Nucleic Acids Res, 34, 647-658.  
17028278 J.Wiethaus, A.Wirsing, F.Narberhaus, and B.Masepohl (2006).
Overlapping and specialized functions of the molybdenum-dependent regulators MopA and MopB in Rhodobacter capsulatus.
  J Bacteriol, 188, 8441-8451.  
15704013 W.A.McLaughlin, D.W.Kulp, J.de la Cruz, X.J.Lu, C.L.Lawson, and H.M.Berman (2004).
A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction.
  J Struct Funct Genomics, 5, 255-265.  
14641908 D.J.Studholme, and R.N.Pau (2003).
A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea.
  BMC Microbiol, 3, 24.  
14573954 F.Dall'Antonia, P.J.Baker, and T.R.Schneider (2003).
Optimization of selenium substructures as obtained from SHELXD.
  Acta Crystallogr D Biol Crystallogr, 59, 1987-1994.  
12583917 J.Kuper, S.Meyer zu Berstenhorst, B.Vödisch, R.R.Mendel, G.Schwarz, and D.H.Boxer (2003).
In vivo detection of molybdate-binding proteins using a competition assay with ModE in Escherichia coli.
  FEMS Microbiol Lett, 218, 187-193.  
12595552 J.Zaim, and A.M.Kierzek (2003).
The structure of full-length LysR-type transcriptional regulators. Modeling of the full-length OxyR transcription factor dimer.
  Nucleic Acids Res, 31, 1444-1454.  
12615898 L.Lu, J.Vollmer, C.Moulon, H.U.Weltzien, P.Marrack, and J.Kappler (2003).
Components of the ligand for a Ni++ reactive human T cell clone.
  J Exp Med, 197, 567-574.  
11836258 A.W.Schüttelkopf, J.A.Harrison, D.H.Boxer, and W.N.Hunter (2002).
Passive acquisition of ligand by the MopII molbindin from Clostridium pasteurianum: structures of apo and oxyanion-bound forms.
  J Biol Chem, 277, 15013-15020.
PDB codes: 1gug 1gun 1guo 1gus 1gut
11839496 J.L.Huffman, and R.G.Brennan (2002).
Prokaryotic transcription regulators: more than just the helix-turn-helix motif.
  Curr Opin Struct Biol, 12, 98.  
12029041 P.M.McNicholas, and R.P.Gunsalus (2002).
The molybdate-responsive Escherichia coli ModE transcriptional regulator coordinates periplasmic nitrate reductase (napFDAGHBC) operon expression with nitrate and molybdate availability.
  J Bacteriol, 184, 3253-3259.  
11679755 J.A.Harrison, A.W.Schüttelkopf, D.H.Boxer, and W.N.Hunter (2001).
Crystallization and X-ray diffraction measurements on recombinant molbindin, MopII, from Clostridium pasteurianum.
  Acta Crystallogr D Biol Crystallogr, 57, 1715-1717.  
11013219 D.M.van Aalten, C.C.DiRusso, J.Knudsen, and R.K.Wierenga (2000).
Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold.
  EMBO J, 19, 5167-5177.
PDB code: 1e2x
11092866 L.A.Anderson, E.McNairn, T.Lubke, R.N.Pau, D.H.Boxer, and T.Leubke (2000).
ModE-dependent molybdate regulation of the molybdenum cofactor operon moa in Escherichia coli.
  J Bacteriol, 182, 7035-7043.  
11080635 U.G.Wagner, E.Stupperich, and C.Kratky (2000).
Structure of the molybdate/tungstate binding protein mop from Sporomusa ovata.
  Structure, 8, 1127-1136.
PDB code: 1fr3
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.

 

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