5x50: Difference between revisions

Latest revision as of 07:54, 22 November 2023

RNA Polymerase II from Komagataella Pastoris (Type-2 crystal)

Structural highlights

5x50 is a 10 chain structure with sequence from Komagataella phaffii CBS 7435 and Komagataella phaffii GS115. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 4.293Å
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C4R4Y0_KOMPG DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279]

Publication Abstract from PubMed

RNA polymerase II (Pol II) is a 12-subunit protein complex that conducts the transcription of mRNA and some small RNAs. In this work, the crystal structure of Pol II from the methylotropic yeast Komagataella pastoris (Pichia pastoris) was determined. While the structure is highly homologous to that of Pol II from the budding yeast Saccharomyces cerevisiae, the stalk and clamp modules of the K. pastoris Pol II displayed large inward rotations, closing the central cleft to a greater extent than in the known S. cerevisiae Pol II structures. The conformational differences reflect the inherent flexibilities of the stalk and the clamp, as additional low-resolution structures of K. pastoris Pol II in different crystal forms revealed diverse stalk and clamp orientations. Comparisons with other eukaryotic/archaeal RNA polymerase structures in the Protein Data Bank revealed the distributions of the stalk and clamp orientations. The conformational plasticity should be essential for transcriptional functions and binding various regulatory factors.

Crystal structure of RNA polymerase II from Komagataella pastoris.,Ehara H, Umehara T, Sekine SI, Yokoyama S Biochem Biophys Res Commun. 2017 May 27;487(2):230-235. doi:, 10.1016/j.bbrc.2017.04.039. Epub 2017 Apr 12. PMID:28412353^[1]

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

References

↑ Ehara H, Umehara T, Sekine SI, Yokoyama S. Crystal structure of RNA polymerase II from Komagataella pastoris. Biochem Biophys Res Commun. 2017 May 27;487(2):230-235. doi:, 10.1016/j.bbrc.2017.04.039. Epub 2017 Apr 12. PMID:28412353 doi:https://dx.doi.org/10.1016/j.bbrc.2017.04.039

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OCA

[1] Ehara H, Umehara T, Sekine SI, Yokoyama S. Crystal structure of RNA polymerase II from Komagataella pastoris. Biochem Biophys Res Commun. 2017 May 27;487(2):230-235. doi:, 10.1016/j.bbrc.2017.04.039. Epub 2017 Apr 12. PMID:28412353 doi:https://dx.doi.org/10.1016/j.bbrc.2017.04.039

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5x50' size='340' side='right'caption='[[5x50]], [[Resolution|resolution]] 4.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5x50]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X50 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X50 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5x50]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_phaffii_CBS_7435 Komagataella phaffii CBS 7435] and [https://en.wikipedia.org/wiki/Komagataella_phaffii_GS115 Komagataella phaffii GS115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X50 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X50 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 4.293&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x4z|5x4z]], [[5x51|5x51]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5x50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x50 OCA], [https://pdbe.org/5x50 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x50 RCSB], [https://www.ebi.ac.uk/pdbsum/5x50 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x50 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=5x50 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x50 OCA], [http://pdbe.org/5x50 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x50 RCSB], [http://www.ebi.ac.uk/pdbsum/5x50 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x50 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586] [[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279]
+[https://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Komagataella phaffii CBS 7435]]
-[[Category: Kompc]]
+[[Category: Komagataella phaffii GS115]]
-[[Category: Kompg]]
 [[Category: Large Structures]]
-[[Category: Ehara, H]]
+[[Category: Ehara H]]
-[[Category: Sekine, S]]
+[[Category: Sekine S]]
-[[Category: Umehara, T]]
+[[Category: Umehara T]]
-[[Category: Yokoyama, S]]
+[[Category: Yokoyama S]]
-[[Category: Rna polymerase]]
-[[Category: Transcription]]
-[[Category: Transferase]]

5x50: Difference between revisions

Latest revision as of 07:54, 22 November 2023

RNA Polymerase II from Komagataella Pastoris (Type-2 crystal)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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