This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4jk2

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 02:22, 5 August 2016

X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp)

Structural highlights

4jk2 is a 12 chain structure with sequence from Ecoli and Escherichia coli mds42. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	4igc, 4jk1
Gene:	rpoA, pez, phs, sez, b3295, JW3257 (ECOLI), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 (ECOLI), rpoC, tabB, b3988, JW3951 (ECOLI), rpoZ, ECMDS42_3083 (Escherichia coli MDS42), rpoD, alt, b3067, JW3039 (ECOLI)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[H0QDQ9_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 (By similarity).[HAMAP-Rule:MF_00366][SAAS:SAAS003716_004_017283] [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

Both ppGpp and pppGpp are thought to function collectively as second messengers for many complex cellular responses to nutritional stress throughout biology. There are few indications that their regulatory effects might be different; however, this question has been largely unexplored for lack of an ability to experimentally manipulate the relative abundance of ppGpp and pppGpp. Here, we achieve preferential accumulation of either ppGpp or pppGpp with Escherichia coli strains through induction of different Streptococcal (p)ppGpp synthetase fragments. In addition, expression of E. coli GppA, a pppGpp 5'-gamma phosphate hydrolase that converts pppGpp to ppGpp, is manipulated to fine tune differential accumulation of ppGpp and pppGpp. In vivo and in vitro experiments show that pppGpp is less potent than ppGpp with respect to regulation of growth rate, RNA/DNA ratios, ribosomal RNA P1 promoter transcription inhibition, threonine operon promoter activation and RpoS induction. To provide further insights into regulation by (p)ppGpp, we have also determined crystal structures of E. coli RNA polymerase-sigma70 holoenzyme with ppGpp and pppGpp. We find that both nucleotides bind to a site at the interface between beta' and omega subunits.

Differential regulation by ppGpp versus pppGpp in Escherichia coli.,Mechold U, Potrykus K, Murphy H, Murakami KS, Cashel M Nucleic Acids Res. 2013 Apr 25. PMID:23620295^[1]

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

References

↑ Mechold U, Potrykus K, Murphy H, Murakami KS, Cashel M. Differential regulation by ppGpp versus pppGpp in Escherichia coli. Nucleic Acids Res. 2013 Apr 25. PMID:23620295 doi:10.1093/nar/gkt302

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/4jk2"

@@ Line 1: / Line 1: @@
 ==X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp)==
 <StructureSection load='4jk2' size='340' side='right' caption='[[4jk2]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4jk2]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12] and [http://en.wikipedia.org/wiki/Escherichia_coli_str._k-12_substr._mds42 Escherichia coli str. k-12 substr. mds42]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JK2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JK2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4jk2]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_mds42 Escherichia coli mds42]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JK2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JK2 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0O2:GUANOSINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)+3-(TRIHYDROGEN+DIPHOSPHATE)'>0O2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4igc|4igc]], [[4jk1|4jk1]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), 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=83333 Escherichia coli K-12]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), rpoZ, ECMDS42_3083 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1110693 Escherichia coli str. K-12 substr. MDS42]), rpoD, alt, b3067, JW3039 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), 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=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ, ECMDS42_3083 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1110693 Escherichia coli MDS42]), rpoD, alt, b3067, JW3039 ([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=4jk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jk2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jk2 RCSB], [http://www.ebi.ac.uk/pdbsum/4jk2 PDBsum]</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=4jk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jk2 OCA], [http://pdbe.org/4jk2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jk2 RCSB], [http://www.ebi.ac.uk/pdbsum/4jk2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jk2 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4jk2" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[RNA polymerase|RNA polymerase]]
+*[[Sigma factor|Sigma factor]]
 == References ==
 <references/>
@@ Line 27: / Line 30: @@
 </StructureSection>
 [[Category: DNA-directed RNA polymerase]]
-[[Category: Escherichia coli k-12]]
+[[Category: Ecoli]]
-[[Category: Escherichia coli str. k-12 substr. mds42]]
+[[Category: Escherichia coli mds42]]
 [[Category: Murakami, K S]]
 [[Category: Dna]]
 [[Category: Transcription]]
 [[Category: Transferase]]

4jk2

From Proteopedia

Revision as of 02:22, 5 August 2016

X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox