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5ms0

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Revision as of 21:06, 10 April 2020

pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM

5ms0, resolution 9.80Å

Structural highlights

5ms0 is a 14 chain structure with sequence from [1] and "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	N, lambdap49 ("Bacillus coli" Migula 1895), nusB, groNB, ssyB, b0416, JW0406 ("Bacillus coli" Migula 1895), nusA, b3169, JW3138 ("Bacillus coli" Migula 1895), rpoZ, b3649, JW3624 ("Bacillus coli" Migula 1895), rpoA, pez, phs, sez, b3295, JW3257 ("Bacillus coli" Migula 1895), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ("Bacillus coli" Migula 1895), rpoC, tabB, b3988, JW3951 ("Bacillus coli" Migula 1895), rpsJ, nusE, b3321, JW3283 ("Bacillus coli" Migula 1895), nusG, b3982, JW3945 ("Bacillus coli" Migula 1895)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RS10_ECOLI] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [NUSB_ECOLI] One of the proteins essential for the formation of the RNA polymerase antitermination complex in the presence of lambda phage N protein. However, it is involved in the transcription termination process at certain sites during normal bacterial growth. Binds to the BoxA RNA motif. [RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [NUSG_ECOLI] Participates in transcription elongation, termination and antitermination. In the absence of Rho, increases the rate of transcription elongation by the RNA polymerase (RNAP), probably by partially suppressing pausing. In the presence of Rho, modulates most Rho-dependent termination events by interacting with the RNAP to render the complex more susceptible to the termination activity of Rho. May be required to overcome a kinetic limitation of Rho to function at certain terminators. Also involved in ribosomal RNA and phage lambda N-mediated transcriptional antitermination.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] [NUSA_ECOLI] Participates in both transcription termination and antitermination. Involved in a variety of cellular and viral termination and antitermination processes, such as Rho-dependent transcriptional termination, intrinsic termination, and phage lambda N-mediated transcriptional antitermination. Also important for coordinating the cellular responses to DNA damage by coupling the processes of nucleotide excision repair and translesion synthesis to transcription.^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18] [REGN_LAMBD] Antitermination proteins positively regulate expression of the phage early and late gene operons. Bacterial host RNA polymerase modified by these antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes. N protein regulates the transition from the early to the middle stage of lytic development. It is a transcription antitermination protein that prevents termination at the rho-dependent tL and tR transcription termination sites. [RPOB_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [RPOZ_ECOLI] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.[HAMAP-Rule:MF_00366] [RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]

Publication Abstract from PubMed

lambdaN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein lambdaN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The structural basis of the process has so far remained elusive. Here we describe a crystal structure of a lambdaN-NusA-NusB-NusE-nut site complex and an electron cryo-microscopic structure of a complete transcription antitermination complex, comprising RNA polymerase, DNA, nut site RNA, all Nus factors and lambdaN, validated by crosslinking/mass spectrometry. Due to intrinsic disorder, lambdaN can act as a multiprotein/RNA interaction hub, which, together with nut site RNA, arranges NusA, NusB and NusE into a triangular complex. This complex docks via the NusA N-terminal domain and the lambdaN C-terminus next to the RNA exit channel on RNA polymerase. Based on the structures, comparative crosslinking analyses and structure-guided mutagenesis, we hypothesize that lambdaN mounts a multipronged strategy to reprogram the transcriptional machinery, which may include (1) the lambdaN C terminus clamping the RNA exit channel, thus stabilizing the DNA:RNA hybrid; (2) repositioning of NusA and RNAP elements, thus redirecting nascent RNA and sequestering the upstream branch of a terminator hairpin; and (3) hindering RNA engagement of termination factor rho and/or obstructing rho translocation on the transcript.

Structural basis for lambdaN-dependent processive transcription antitermination.,Said N, Krupp F, Anedchenko E, Santos KF, Dybkov O, Huang YH, Lee CT, Loll B, Behrmann E, Burger J, Mielke T, Loerke J, Urlaub H, Spahn CMT, Weber G, Wahl MC Nat Microbiol. 2017 Apr 28;2:17062. doi: 10.1038/nmicrobiol.2017.62. PMID:28452979^[19]

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

References

↑ Li J, Horwitz R, McCracken S, Greenblatt J. NusG, a new Escherichia coli elongation factor involved in transcriptional antitermination by the N protein of phage lambda. J Biol Chem. 1992 Mar 25;267(9):6012-9. PMID:1532577
↑ Sullivan SL, Gottesman ME. Requirement for E. coli NusG protein in factor-dependent transcription termination. Cell. 1992 Mar 6;68(5):989-94. PMID:1547498
↑ Nehrke KW, Zalatan F, Platt T. NusG alters rho-dependent termination of transcription in vitro independent of kinetic coupling. Gene Expr. 1993;3(2):119-33. PMID:7505669
↑ Li J, Mason SW, Greenblatt J. Elongation factor NusG interacts with termination factor rho to regulate termination and antitermination of transcription. Genes Dev. 1993 Jan;7(1):161-72. PMID:8422985
↑ Burova E, Hung SC, Sagitov V, Stitt BL, Gottesman ME. Escherichia coli NusG protein stimulates transcription elongation rates in vivo and in vitro. J Bacteriol. 1995 Mar;177(5):1388-92. PMID:7868616
↑ Burns CM, Richardson JP. NusG is required to overcome a kinetic limitation to Rho function at an intragenic terminator. Proc Natl Acad Sci U S A. 1995 May 23;92(11):4738-42. PMID:7761393
↑ Zellars M, Squires CL. Antiterminator-dependent modulation of transcription elongation rates by NusB and NusG. Mol Microbiol. 1999 Jun;32(6):1296-304. PMID:10383769
↑ Pasman Z, von Hippel PH. Regulation of rho-dependent transcription termination by NusG is specific to the Escherichia coli elongation complex. Biochemistry. 2000 May 9;39(18):5573-85. PMID:10820031
↑ Torres M, Balada JM, Zellars M, Squires C, Squires CL. In vivo effect of NusB and NusG on rRNA transcription antitermination. J Bacteriol. 2004 Mar;186(5):1304-10. PMID:14973028
↑ Greenblatt J, Li J. Interaction of the sigma factor and the nusA gene protein of E. coli with RNA polymerase in the initiation-termination cycle of transcription. Cell. 1981 May;24(2):421-8. PMID:6263495
↑ Greenblatt J, McLimont M, Hanly S. Termination of transcription by nusA gene protein of Escherichia coli. Nature. 1981 Jul 16;292(5820):215-20. PMID:6265785
↑ Schmidt MC, Chamberlin MJ. Amplification and isolation of Escherichia coli nusA protein and studies of its effects on in vitro RNA chain elongation. Biochemistry. 1984 Jan 17;23(2):197-203. PMID:6199039
↑ Schmidt MC, Chamberlin MJ. nusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites. J Mol Biol. 1987 Jun 20;195(4):809-18. PMID:2821282 doi:http://dx.doi.org/10.1016/0022-2836(87)90486-4
↑ Liu K, Hanna MM. NusA contacts nascent RNA in Escherichia coli transcription complexes. J Mol Biol. 1995 Apr 7;247(4):547-58. PMID:7536848 doi:http://dx.doi.org/10.1006/jmbi.1994.0161
↑ Vogel U, Jensen KF. NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA. J Biol Chem. 1997 May 9;272(19):12265-71. PMID:9139668
↑ Gusarov I, Nudler E. Control of intrinsic transcription termination by N and NusA: the basic mechanisms. Cell. 2001 Nov 16;107(4):437-49. PMID:11719185
↑ Cohen SE, Lewis CA, Mooney RA, Kohanski MA, Collins JJ, Landick R, Walker GC. Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15517-22. doi:, 10.1073/pnas.1005203107. Epub 2010 Aug 9. PMID:20696893 doi:http://dx.doi.org/10.1073/pnas.1005203107
↑ Burmann BM, Rosch P. The role of E. coli Nus-factors in transcription regulation and transcription:translation coupling: From structure to mechanism. Transcription. 2011 May;2(3):130-134. PMID:21922055 doi:http://dx.doi.org/10.4161/trns.2.3.15671
↑ Said N, Krupp F, Anedchenko E, Santos KF, Dybkov O, Huang YH, Lee CT, Loll B, Behrmann E, Burger J, Mielke T, Loerke J, Urlaub H, Spahn CMT, Weber G, Wahl MC. Structural basis for lambdaN-dependent processive transcription antitermination. Nat Microbiol. 2017 Apr 28;2:17062. doi: 10.1038/nmicrobiol.2017.62. PMID:28452979 doi:http://dx.doi.org/10.1038/nmicrobiol.2017.62

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ms0"

@@ Line 3: / Line 3: @@
 <SX load='5ms0' size='340' side='right' viewer='molstar' caption='[[5ms0]], [[Resolution|resolution]] 9.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ms0]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MS0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MS0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ms0]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MS0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MS0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">N, lambdap49 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), nusB, groNB, ssyB, b0416, JW0406 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), nusA, b3169, JW3138 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsJ, nusE, b3321, JW3283 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), nusG, b3982, JW3945 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=5ms0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms0 OCA], [http://pdbe.org/5ms0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ms0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ms0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms0 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ms0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms0 OCA], [http://pdbe.org/5ms0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ms0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ms0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms0 ProSAT]</span></td></tr>
 </table>
 == Function ==

5ms0

From Proteopedia

Revision as of 21:06, 10 April 2020

pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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