1g4d: Difference between revisions

Latest revision as of 08:30, 22 May 2024

NMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAIN/DNA COMPLEX

Structural highlights

1g4d is a 3 chain structure with sequence from Escherichia virus Mu. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

REPC_BPMU Promotes latency by binding operators O1 and O2 in the enhancer/operator region, thereby repressing the transcription from the Pe (early) promoter and blocking the expression of the genes required for replication (lytic growth). Competes with DDE-recombinase A for binding to the internal activation sequence (IAS), which overlaps O1 and O2. The outcome of this competition determines if the virus enters latency or starts replication. Makes the cell immune to superinfection by repressing genes expression of any subsequent incoming viral genome.^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

We have determined the solution structure of the complex between the 'winged-helix' enhancer binding domain of the Mu repressor protein and its cognate DNA site. The structure reveals an unusual use for the 'wing' which becomes immobilized upon DNA binding where it makes intermolecular hydrogen bond contacts deep within the minor groove. Although the wing is mobile in the absence of DNA, it partially negates the large entropic penalty associated with its burial by maintaining a small degree of structural order in the DNA-free state. Extensive contacts are also formed between the recognition helix and the DNA, which reads the major groove of a highly conserved region of the binding site through a single base-specific hydrogen bond and van der Waals contacts.

The Mu repressor-DNA complex contains an immobilized 'wing' within the minor groove.,Wojciak JM, Iwahara J, Clubb RT Nat Struct Biol. 2001 Jan;8(1):84-90. PMID:11135677^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ranquet C, Geiselmann J, Toussaint A. The tRNA function of SsrA contributes to controlling repression of bacteriophage Mu prophage. Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10220-5. PMID:11517307 doi:10.1073/pnas.171620598
↑ O'Handley D, Nakai H. Derepression of bacteriophage mu transposition functions by truncated forms of the immunity repressor. J Mol Biol. 2002 Sep 13;322(2):311-24. PMID:12217693 doi:10.1016/s0022-2836(02)00755-6
↑ Ranquet C, Toussaint A, de Jong H, Maenhaut-Michel G, Geiselmann J. Control of bacteriophage mu lysogenic repression. J Mol Biol. 2005 Oct 14;353(1):186-95. PMID:16154589 doi:10.1016/j.jmb.2005.08.015
↑ Marshall-Batty KR, Nakai H. Activation of a dormant ClpX recognition motif of bacteriophage Mu repressor by inducing high local flexibility. J Biol Chem. 2008 Apr 4;283(14):9060-70. PMID:18230617 doi:10.1074/jbc.M705508200
↑ Kahmeyer-Gabbe M, Howe MM. Regulatory factors acting at the bacteriophage Mu middle promoter. J Bacteriol. 1996 Mar;178(6):1585-92. PMID:8626285 doi:10.1128/jb.178.6.1585-1592.1996
↑ Wojciak JM, Iwahara J, Clubb RT. The Mu repressor-DNA complex contains an immobilized 'wing' within the minor groove. Nat Struct Biol. 2001 Jan;8(1):84-90. PMID:11135677 doi:10.1038/83103

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Ranquet C, Geiselmann J, Toussaint A. The tRNA function of SsrA contributes to controlling repression of bacteriophage Mu prophage. Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10220-5. PMID:11517307 doi:10.1073/pnas.171620598

[2] O'Handley D, Nakai H. Derepression of bacteriophage mu transposition functions by truncated forms of the immunity repressor. J Mol Biol. 2002 Sep 13;322(2):311-24. PMID:12217693 doi:10.1016/s0022-2836(02)00755-6

[3] Ranquet C, Toussaint A, de Jong H, Maenhaut-Michel G, Geiselmann J. Control of bacteriophage mu lysogenic repression. J Mol Biol. 2005 Oct 14;353(1):186-95. PMID:16154589 doi:10.1016/j.jmb.2005.08.015

[4] Marshall-Batty KR, Nakai H. Activation of a dormant ClpX recognition motif of bacteriophage Mu repressor by inducing high local flexibility. J Biol Chem. 2008 Apr 4;283(14):9060-70. PMID:18230617 doi:10.1074/jbc.M705508200

[5] Kahmeyer-Gabbe M, Howe MM. Regulatory factors acting at the bacteriophage Mu middle promoter. J Bacteriol. 1996 Mar;178(6):1585-92. PMID:8626285 doi:10.1128/jb.178.6.1585-1592.1996

[6] Wojciak JM, Iwahara J, Clubb RT. The Mu repressor-DNA complex contains an immobilized 'wing' within the minor groove. Nat Struct Biol. 2001 Jan;8(1):84-90. PMID:11135677 doi:10.1038/83103

[1]

[2]

[3]

[4]

[5]

[6]

@@ Line 1: / Line 1: @@
 ==NMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAIN/DNA COMPLEX==
-<StructureSection load='1g4d' size='340' side='right' caption='[[1g4d]], [[NMR_Ensembles_of_Models | 25 NMR models]]' scene=''>
+<StructureSection load='1g4d' size='340' side='right'caption='[[1g4d]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1g4d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpmu Bpmu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G4D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1g4d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Mu Escherichia virus Mu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G4D FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qpm|1qpm]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MU C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10677 BPMU])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4d OCA], [https://pdbe.org/1g4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g4d RCSB], [https://www.ebi.ac.uk/pdbsum/1g4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4d ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1g4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4d OCA], [http://pdbe.org/1g4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g4d RCSB], [http://www.ebi.ac.uk/pdbsum/1g4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4d ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/REPC_BPMU REPC_BPMU] Promotes latency by binding operators O1 and O2 in the enhancer/operator region, thereby repressing the transcription from the Pe (early) promoter and blocking the expression of the genes required for replication (lytic growth). Competes with DDE-recombinase A for binding to the internal activation sequence (IAS), which overlaps O1 and O2. The outcome of this competition determines if the virus enters latency or starts replication. Makes the cell immune to superinfection by repressing genes expression of any subsequent incoming viral genome.<ref>PMID:11517307</ref> <ref>PMID:12217693</ref> <ref>PMID:16154589</ref> <ref>PMID:18230617</ref> <ref>PMID:8626285</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Bpmu]]
+[[Category: Escherichia virus Mu]]
-[[Category: Clubb, R T]]
+[[Category: Large Structures]]
-[[Category: Iwahara, J]]
+[[Category: Clubb RT]]
-[[Category: Wojciak, J M]]
+[[Category: Iwahara J]]
-[[Category: Bacteriophage mu]]
+[[Category: Wojciak JM]]
-[[Category: Helix-turn-helix]]
-[[Category: Protein-dna complex]]
-[[Category: Repressor]]
-[[Category: Viral protein-dna complex]]
-[[Category: Virus/viral protein]]
-[[Category: Winged-helix]]

1g4d: Difference between revisions

Latest revision as of 08:30, 22 May 2024

NMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAIN/DNA COMPLEX

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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