2pi4
From Proteopedia
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|PDB= 2pi4 |SIZE=350|CAPTION= <scene name='initialview01'>2pi4</scene>, resolution 2.50Å | |PDB= 2pi4 |SIZE=350|CAPTION= <scene name='initialview01'>2pi4</scene>, resolution 2.50Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=GH3:3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE'>GH3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <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> |
| - | |GENE= 1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= 1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2pi5|2PI5]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pi4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pi4 OCA], [http://www.ebi.ac.uk/pdbsum/2pi4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pi4 RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2PI4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2PI4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PI4 OCA]. |
==Reference== | ==Reference== | ||
Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase., Kennedy WP, Momand JR, Yin YW, J Mol Biol. 2007 Jul 6;370(2):256-68. Epub 2007 Mar 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17512007 17512007] | Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase., Kennedy WP, Momand JR, Yin YW, J Mol Biol. 2007 Jul 6;370(2):256-68. Epub 2007 Mar 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17512007 17512007] | ||
| - | [[Category: Bacteriophage t7]] | ||
[[Category: DNA-directed RNA polymerase]] | [[Category: DNA-directed RNA polymerase]] | ||
| + | [[Category: Enterobacteria phage t7]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Kennedy, W P.]] | [[Category: Kennedy, W P.]] | ||
[[Category: Momand, J R.]] | [[Category: Momand, J R.]] | ||
[[Category: Yin, Y W.]] | [[Category: Yin, Y W.]] | ||
| - | [[Category: GH3]] | ||
| - | [[Category: MG]] | ||
[[Category: initiating nucleotides.]] | [[Category: initiating nucleotides.]] | ||
[[Category: t7 rna polymerase]] | [[Category: t7 rna polymerase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:36:08 2008'' |
Revision as of 01:36, 31 March 2008
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| , resolution 2.50Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Gene: | 1 (Enterobacteria phage T7) | ||||||
| Activity: | DNA-directed RNA polymerase, with EC number 2.7.7.6 | ||||||
| Related: | 2PI5
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T7RNAP complexed with a phi10 protein and initiating GTPs.
Overview
DNA-directed RNA polymerases are capable of initiating synthesis of RNA without primers, the first catalytic stage of initiation is referred to as de novo RNA synthesis. De novo synthesis is a unique phase in the transcription cycle where the RNA polymerase binds two nucleotides rather than a nascent RNA polymer and a single nucleotide. For bacteriophage T7 RNA polymerase, transcription begins with a marked preference for GTP at the +1 and +2 positions. We determined the crystal structures of T7 RNA polymerase complexes captured during the de novo RNA synthesis. The DNA substrates in the structures in the complexes contain a common Phi 10 duplex promoter followed by a unique five base single-stranded extension of template DNA whose sequences varied at positions +1 and +2, thereby allowing for different pairs of initiating nucleotides GTP, ATP, CTP or UTP to bind. The structures show that the initiating nucleotides bind RNA polymerase in locations distinct from those described previously for elongation complexes. Selection bias in favor of GTP as an initiating nucleotide is accomplished by shape complementarity, extensive protein side-chain and strong base-stacking interactions for the guanine moiety in the enzyme active site. Consequently, an initiating GTP provides the largest stabilization force for the open promoter conformation.
About this Structure
2PI4 is a Single protein structure of sequence from Enterobacteria phage t7. Full crystallographic information is available from OCA.
Reference
Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase., Kennedy WP, Momand JR, Yin YW, J Mol Biol. 2007 Jul 6;370(2):256-68. Epub 2007 Mar 21. PMID:17512007
Page seeded by OCA on Mon Mar 31 04:36:08 2008
