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PDBsum entry 1rr7

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protein metals links
Transcription PDB id
1rr7
Jmol
Contents
Protein chain
94 a.a. *
Metals
_PT ×2
Waters ×22
* Residue conservation analysis
PDB id:
1rr7
Name: Transcription
Title: Crystal structure of the middle operon regulator protein of bacteriophage mu
Structure: Middle operon regulator. Chain: a. Fragment: middle operon regulator protein. Synonym: protein mor, protein e17. Engineered: yes
Source: Enterobacteria phage mu. Organism_taxid: 10677. Gene: mor. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.252     R-free:   0.268
Authors: M.Kumaraswami,M.M.Howe,H.W.Park
Key ref:
M.Kumaraswami et al. (2004). Crystal structure of the Mor protein of bacteriophage Mu, a member of the Mor/C family of transcription activators. J Biol Chem, 279, 16581-16590. PubMed id: 14729670 DOI: 10.1074/jbc.M313555200
Date:
08-Dec-03     Release date:   17-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23848  (VMOR_BPMU) -  Middle operon regulator
Seq:
Struc:
129 a.a.
94 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1074/jbc.M313555200 J Biol Chem 279:16581-16590 (2004)
PubMed id: 14729670  
 
 
Crystal structure of the Mor protein of bacteriophage Mu, a member of the Mor/C family of transcription activators.
M.Kumaraswami, M.M.Howe, H.W.Park.
 
  ABSTRACT  
 
Transcription from the middle promoter, Pm, of bacteriophage Mu requires the phage-encoded activator protein Mor and bacterial RNA polymerase. Mor is a sequence-specific DNA-binding protein that mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. Here we present the first structure for a member of the Mor/C family of transcription activators, the crystal structure of Mor to 2.2-A resolution. Each monomer of the Mor dimer is composed of two domains, the N-terminal dimerization domain and C-terminal DNA-binding domain, which are connected by a linker containing a beta strand. The N-terminal dimerization domain has an unusual mode of dimerization; helices alpha1 and alpha2 of both monomers are intertwined to form a four-helix bundle, generating a hydrophobic core that is further stabilized by antiparallel interactions between the two beta strands. Mutational analysis of key leucine residues in helix alpha1 demonstrated a role for this hydrophobic core in protein solubility and function. The C-terminal domain has a classical helix-turn-helix DNA-binding motif that is located at opposite ends of the elongated dimer. Since the distance between the two helix-turn-helix motifs is too great to allow binding to two adjacent major grooves of the 16-bp Mor-binding site, we propose that conformational changes in the protein and DNA will be required for Mor to interact with the DNA. The highly conserved glycines flanking the beta strand may act as pivot points, facilitating the conformational changes of Mor, and the DNA may be bent.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Structure of Mor. A, ribbon representation of the Mor dimer viewed parallel to the crystallographic 2-fold axis. One monomer is colored red and the other yellow. The secondary structure elements, helices 1-5 and strand 1, are numbered according to their relative position from the N terminus; those in the second monomer are identified with a prime. B, one layer of hydrophobic interactions in the dimerization domain. One circular layer of hydrophobic interactions involving the side chains of Leu35 and Ile^60 of both monomers is presented, with the side chains shown in the ball-and- stick representation and colored red. C, key glycine, tyrosine, and glutamine residues in the dimerization domain. The dimerization domain is tilted with respect to those in A and B; the Gln68 and Tyr70 side chains are shown in the ball-and- stick representation and colored red, and the glycine residues are marked with red spheres. The residues are shown in both monomers, but only one residue per pair is identified. D, superimposition of the HTH motifs of Mor (red) and TrpR (gray). The HTH motif is rotated relative to that in A, and the helices are labeled as in Mor. E, the helix-turn-helix DNA-binding motif. The HTH motif shown is rotated with respect to those in A and D. The three helices making up the HTH motif, 3, 4, and 5 are shown as ribbons; the side chains of amino acids that are predicted to be involved in DNA-base recognition are shown in the ball-and-stick representation. Figs. 2 and 3 were generated using the program RIBBONS (47).
Figure 4.
FIG. 4. Electrostatic surface potentials and conformational changes of Mor. A, surface residues are color-coded according to their charge as follows: blue for positive electrostatic potential and red for negative electrostatic potential. The view shown is 90° vertical rotation, relative to that in Fig. 2A. B, the Mor dimerization domain is represented with cylinders for -helices and arrows for -strands. The Mor HTH motifs are shown as ribbon diagrams. A 20-bp segment of B-DNA is drawn at the top, with arrows showing the Mor HTH motif region that must interact with the two adjacent major grooves of DNA. C, the diagram is as in B except that an 18-bp segment of DNA with an 40° bend is shown with the Mor HTH docked into the major grooves. A was generated using the program GRASP (62).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 16581-16590) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20946386 M.L.Smith, L.N.Avanigadda, P.W.Liddell, K.M.Kenwright, and M.M.Howe (2010).
Identification of the J and K genes in the bacteriophage Mu genome sequence.
  FEMS Microbiol Lett, 313, 29-32.  
18689515 K.Yamada, J.Kaneko, Y.Kamio, and Y.Itoh (2008).
Binding sequences for RdgB, a DNA damage-responsive transcriptional activator, and temperature-dependent expression of bacteriocin and pectin lyase genes in Pectobacterium carotovorum subsp. carotovorum.
  Appl Environ Microbiol, 74, 6017-6025.  
18838393 Y.Jiang, and M.M.Howe (2008).
Regional mutagenesis of the gene encoding the phage Mu late gene activator C identifies two separate regions important for DNA binding.
  Nucleic Acids Res, 36, 6396-6405.  
  17620727 K.K.Shanmuganatham, M.Ravichandran, M.M.Howe, and H.W.Park (2007).
Crystallization and preliminary X-ray analysis of phage Mu activator protein C in a complex with promoter DNA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 620-623.  
15547256 J.Ma, and M.M.Howe (2004).
Binding of the C-terminal domain of the alpha subunit of RNA polymerase to the phage mu middle promoter.
  J Bacteriol, 186, 7858-7864.  
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.