4mex

From Proteopedia

(Difference between revisions)

Revision as of 08:57, 10 April 2019

Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A

Structural highlights

4mex is a 14 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:	, , , , ,
Related:	4mey
Gene:	b3295, BN17_32291, ECs4160, JW3257, LF82_1958, pez, phs, rpoA, sez (ECOLI), b3987, groN, JW3950, K758_06833, nitB, rif, ron, rpoB, stl, stv, tabD (ECOLI), b3988, BN17_39521, ECs4911, JW3951, LF82_1960, rpoC, tabB (ECOLI), b3649, BN17_35921, ECs4524, JW3624, LF82_1966, rpoZ (ECOLI), alt, b3067, JW3039, rpoD (ECOLI)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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] [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] [RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [RPOB_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [RPOD_ECOLI] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

Publication Abstract from PubMed

We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center 'bridge-helix cap' comprising the 'bridge-helix N-terminal hinge', 'F-loop', and 'link region'. We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge.DOI: http://dx.doi.org/10.7554/eLife.02451.001.

Transcription inhibition by the depsipeptide antibiotic salinamide A.,Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH Elife. 2014 Apr 30;3:e02451. doi: 10.7554/eLife.02451. PMID:24843001^[1]

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

References

↑ Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH. Transcription inhibition by the depsipeptide antibiotic salinamide A. Elife. 2014 Apr 30;3:e02451. doi: 10.7554/eLife.02451. PMID:24843001 doi:http://dx.doi.org/10.7554/eLife.02451

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/4mex"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A==
-<StructureSection load='4mex' size='340' side='right' caption='[[4mex]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
+<StructureSection load='4mex' size='340' side='right'caption='[[4mex]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4mex]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MEX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MEX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4mex]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MEX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MEX 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>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=28H:(2R,3R)-3-HYDROXY-2,4-DIMETHYLPENTANOIC+ACID'>28H</scene>, <scene name='pdbligand=28J:D-ALLOISOLEUCINE'>28J</scene>, <scene name='pdbligand=28K:(2E)-3-{(2S)-2-[(1R)-1-HYDROXYETHYL]OXIRAN-2-YL}PROP-2-ENOIC+ACID'>28K</scene>, <scene name='pdbligand=2TL:D-ALLOTHREONINE'>2TL</scene>, <scene name='pdbligand=D4P:(2S)-AMINO(4-HYDROXYPHENYL)ACETIC+ACID'>D4P</scene>, <scene name='pdbligand=MEA:N-METHYLPHENYLALANINE'>MEA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mey|4mey]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3295, BN17_32291, ECs4160, JW3257, LF82_1958, pez, phs, rpoA, sez ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b3987, groN, JW3950, K758_06833, nitB, rif, ron, rpoB, stl, stv, tabD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b3988, BN17_39521, ECs4911, JW3951, LF82_1960, rpoC, tabB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), b3649, BN17_35921, ECs4524, JW3624, LF82_1966, rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), alt, b3067, JW3039, rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4mex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mex OCA], [http://pdbe.org/4mex PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mex RCSB], [http://www.ebi.ac.uk/pdbsum/4mex PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mex ProSAT]</span></td></tr>
@@ Line 30: / Line 31: @@
 </StructureSection>
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Arnold, E]]
 [[Category: Ebright, R H]]

4mex

From Proteopedia

Revision as of 08:57, 10 April 2019

Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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