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69 a.a.
Key reference
DOI no: 10.1016/j.jmb.2004.12.025 J Mol Biol 346:689-701 (2005) PubMed id: 15713456
High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila. J.E.McGeehan, S.D.Streeter, I.Papapanagiotou, G.C.Fox, G.G.Kneale. ABSTRACT
Restriction-modification (R-M) systems serve to protect the host bacterium from invading bacteriophage. The multi-component system includes a methyltransferase, which recognizes and methylates a specific DNA sequence, and an endonuclease which recognises the same sequence and cleaves within or close to this site. The endonuclease will only cleave DNA that is unmethylated at the specific site, thus host DNA is protected while non-host DNA is cleaved. However, following DNA replication, expression of the endonuclease must be delayed until the host DNA is appropriately methylated. In many R-M systems, this regulation is achieved at the transcriptional level via the controller protein, or C-protein. We have solved the first X-ray structure of an R-M controller protein, C.AhdI, to 1.69 A resolution using selenomethionine MAD. C.AhdI is part of a Type IIH R-M system from the pathogen Aeromonas hydrophila. The structure reveals an all-alpha protein that contains a classical helix-turn-helix (HTH) domain and can be assigned to the Xre family of transcriptional regulators. Unlike its monomeric structural homologues, an extended helix generates an interface that results in dimerisation of the free protein. The dimer is electrostatically polarised and a positively charged surface corresponds to the position of the DNA recognition helices of the HTH domain. Comparison with the structure of the lambda cI ternary complex suggests that C.AhdI activates transcription through direct contact with the sigma70 subunit of RNA polymerase.
Selected figure(s)
Figure 3.
Figure 3. Topology of C.AhdI: a single subunit of the C.AhdI dimer is shown as a ribbon representation. Each of the five helices are labelled and coloured individually with all turns, bends and loops coloured yellow. The HTH motif is comprised of H2 (the scaffolding helix) and H3 (the recognition helix), coloured blue and red, and the N and C termini are labelled N and C, respectively.Figure 9.
Figure 9. Modelling of the interaction between C.AhdI and region 4 of the s70 subunit: (a) diagram of the crystal structure 1RIO orientated to show the organisation of the l repressor (subunits blue and cyan) and the s70 subunit of RNAP (orange) bound to dsDNA (black and grey).46 (b) Close-up view of the interacting surfaces between the l repressor and the s70 subunit. The key interacting residues of the l repressor, Glu34 and Asp38, are coloured red and blue, respectively. (c) Superposition of C.AhdI (green) on the l repressor in the ternary complex reveals potential interaction contacts with the s70 subunit mediated through the conserved Glu30 residue (red) and Phe34 (blue).The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 346, 689-701) copyright 2005. Figures were selected by an automated process.
Literature references that cite this PDB file's key reference
PubMed id Reference
19336410 E.Bogdanova, M.Zakharova, S.Streeter, J.Taylor, T.Heyduk, G.Kneale, and K.Severinov (2009).
Transcription regulation of restriction-modification system Esp1396I.Nucleic Acids Res, 37, 3354-3366.
19690367 N.Ball, S.D.Streeter, G.G.Kneale, and J.E.McGeehan (2009).
Structure of the restriction-modification controller protein C.Esp1396I.Acta Crystallogr D Biol Crystallogr, 65, 900-905. 19724127 S.D.Streeter, J.E.McGeehan, and G.G.Kneale (2009).
Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I from Citrobacter sp. RFL231.Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 898-901.
19019826 S.Russo, J.E.Schweitzer, T.Polen, M.Bott, and E.Pohl (2009).
Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes.J Biol Chem, 284, 5208-5216.
PDB codes: 3f51 3f52
19056824 V.Sorokin, K.Severinov, and M.S.Gelfand (2009).
Systematic prediction of control proteins and their DNA binding sites.Nucleic Acids Res, 37, 441-451.
18203750 E.Bogdanova, M.Djordjevic, I.Papapanagiotou, T.Heyduk, G.Kneale, and K.Severinov (2008).
Transcription regulation of the type II restriction-modification system AhdI.Nucleic Acids Res, 36, 1429-1442.
18334533 I.Mruk, and R.M.Blumenthal (2008).
Real-time kinetics of restriction-modification gene expression after entry into a new host cell.Nucleic Acids Res, 36, 2581-2593.
18644840 J.E.McGeehan, S.D.Streeter, S.J.Thresh, N.Ball, R.B.Ravelli, and G.G.Kneale (2008).
Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.Nucleic Acids Res, 36, 4778-4787.
PDB code: 3clc
17933763 I.Mruk, P.Rajesh, and R.M.Blumenthal (2007).
Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system.Nucleic Acids Res, 35, 6935-6952.
17426137 I.Papapanagiotou, S.D.Streeter, P.D.Cary, and G.G.Kneale (2007).
DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence.Nucleic Acids Res, 35, 2643-2650.
17675379 M.Miyakoshi, M.Shintani, T.Terabayashi, S.Kai, H.Yamane, and H.Nojiri (2007).
Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1.J Bacteriol, 189, 6849-6860.
16332697 E.Semenova, L.Minakhin, E.Bogdanova, M.Nagornykh, A.Vasilov, T.Heyduk, A.Solonin, M.Zakharova, and K.Severinov (2005).
Transcription regulation of the EcoRV restriction-modification system.Nucleic Acids Res, 33, 6942-6951. 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 codes are shown on the right.
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