4ylp: Difference between revisions

Latest revision as of 03:43, 21 November 2024

E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA

Structural highlights

4ylp is a 27 chain structure with sequence from Escherichia coli and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 5.5Å
Ligands:	GTP, MG, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

Publication Abstract from PubMed

During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for processive RNA synthesis. Here we present the crystal structures of E. coli transcription initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonucleotides at about 6-A resolution. The structures show how RNA polymerase recognizes DNA promoters that contain spacers of different lengths and reveal a bridging interaction between the 5'-triphosphate of the nascent RNA and the sigma factor that may function to stabilize the short RNA-DNA hybrids during the early stage of transcription initiation. The conformation of the RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide insights into the mechanism that controls both the abortive and productive RNA synthesis.

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.,Zuo Y, Steitz TA Mol Cell. 2015 Apr 8. pii: S1097-2765(15)00175-6. doi:, 10.1016/j.molcel.2015.03.010. PMID:25866247^[1]

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

References

↑ Zuo Y, Steitz TA. Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble. Mol Cell. 2015 Apr 8. pii: S1097-2765(15)00175-6. doi:, 10.1016/j.molcel.2015.03.010. PMID:25866247 doi:https://dx.doi.org/10.1016/j.molcel.2015.03.010

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Zuo Y, Steitz TA. Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble. Mol Cell. 2015 Apr 8. pii: S1097-2765(15)00175-6. doi:, 10.1016/j.molcel.2015.03.010. PMID:25866247 doi:https://dx.doi.org/10.1016/j.molcel.2015.03.010

[1]

@@ Line 1: / Line 1: @@
-{{Large structure}}
 ==E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA==
-<StructureSection load='4ylp' size='340' side='right' caption='[[4ylp]], [[Resolution|resolution]] 5.50&Aring;' scene=''>
+<StructureSection load='4ylp' size='340' side='right'caption='[[4ylp]], [[Resolution|resolution]] 5.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ylp]] is a 27 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YLP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YLP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ylp]] is a 27 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YLP 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 5.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[4yln|4yln]], [[4ylo|4ylo]]</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=4ylp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ylp OCA], [https://pdbe.org/4ylp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ylp RCSB], [https://www.ebi.ac.uk/pdbsum/4ylp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ylp ProSAT]</span></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=4ylp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ylp OCA], [http://pdbe.org/4ylp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ylp RCSB], [http://www.ebi.ac.uk/pdbsum/4ylp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ylp ProSAT]</span></td></tr>
 </table>
-{{Large structure}}
 == Function ==
-[[http://www.uniprot.org/uniprot/RPOC_ECO24 RPOC_ECO24]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_ECO24 RPOB_ECO24]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO24 RPOA_ECO24]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO24 RPOZ_ECO24]] 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. [[http://www.uniprot.org/uniprot/RPOD_ECOLI 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.
+[https://www.uniprot.org/uniprot/RPOA_ECOLI 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]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 21: @@
 ==See Also==
-*[[Sigma factor|Sigma factor]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Escherichia coli]]
-[[Category: Steitz, T A]]
+[[Category: Large Structures]]
-[[Category: Zuo, Y]]
+[[Category: Synthetic construct]]
-[[Category: Dna bubble]]
+[[Category: Steitz TA]]
-[[Category: Initiation complex]]
+[[Category: Zuo Y]]
-[[Category: Rna polymerase]]
-[[Category: Transcription-dna-rna complex]]

4ylp: Difference between revisions

Latest revision as of 03:43, 21 November 2024

E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools