6o3w: Difference between revisions

Latest revision as of 07:04, 11 October 2023

Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1

Structural highlights

6o3w is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SEN1_YEAST ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. Directs RNA polymerase II transcription termination on snoRNAs as well as on several short protein-coding genes. May also play a role in transcription-coupled nucleotide excision repair.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

The Nrd1-Nab3-Sen1 (NNS) complex carries out the transcription termination of non-coding RNAs (ncRNAs) by RNA polymerase II (Pol II) in yeast, although the detailed interactions among its subunits remain obscure. Here we have identified three sequence motifs in Sen1 that mediate direct interactions with the Pol II CTD interaction domain (CID) of Nrd1, determined the crystal structures of these Nrd1 interaction motifs (NIMs) bound to the CID, and characterized the interactions in vitro and in yeast. Removal of all three NIMs abolishes NNS complex formation and gives rise to ncRNA termination defects.

Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1.,Zhang Y, Chun Y, Buratowski S, Tong L Structure. 2019 Apr 23. pii: S0969-2126(19)30127-3. doi:, 10.1016/j.str.2019.04.005. PMID:31104813^[7]

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

References

↑ Steinmetz EJ, Conrad NK, Brow DA, Corden JL. RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts. Nature. 2001 Sep 20;413(6853):327-31. PMID:11565036 doi:https://dx.doi.org/10.1038/35095090
↑ Ursic D, Chinchilla K, Finkel JS, Culbertson MR. Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing. Nucleic Acids Res. 2004 Apr 30;32(8):2441-52. Print 2004. PMID:15121901 doi:https://dx.doi.org/10.1093/nar/gkh561
↑ Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell. 2006 Dec 8;24(5):735-46. PMID:17157256 doi:https://dx.doi.org/10.1016/j.molcel.2006.10.023
↑ Steinmetz EJ, Brow DA. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol Cell Biol. 1996 Dec;16(12):6993-7003. PMID:8943355
↑ Ursic D, Himmel KL, Gurley KA, Webb F, Culbertson MR. The yeast SEN1 gene is required for the processing of diverse RNA classes. Nucleic Acids Res. 1997 Dec 1;25(23):4778-85. PMID:9365256
↑ Rasmussen TP, Culbertson MR. The putative nucleic acid helicase Sen1p is required for formation and stability of termini and for maximal rates of synthesis and levels of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Dec;18(12):6885-96. PMID:9819377
↑ Zhang Y, Chun Y, Buratowski S, Tong L. Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1. Structure. 2019 Apr 23. pii: S0969-2126(19)30127-3. doi:, 10.1016/j.str.2019.04.005. PMID:31104813 doi:https://dx.doi.org/10.1016/j.str.2019.04.005

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Steinmetz EJ, Conrad NK, Brow DA, Corden JL. RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts. Nature. 2001 Sep 20;413(6853):327-31. PMID:11565036 doi:https://dx.doi.org/10.1038/35095090

[2] Ursic D, Chinchilla K, Finkel JS, Culbertson MR. Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing. Nucleic Acids Res. 2004 Apr 30;32(8):2441-52. Print 2004. PMID:15121901 doi:https://dx.doi.org/10.1093/nar/gkh561

[3] Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell. 2006 Dec 8;24(5):735-46. PMID:17157256 doi:https://dx.doi.org/10.1016/j.molcel.2006.10.023

[4] Steinmetz EJ, Brow DA. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol Cell Biol. 1996 Dec;16(12):6993-7003. PMID:8943355

[5] Ursic D, Himmel KL, Gurley KA, Webb F, Culbertson MR. The yeast SEN1 gene is required for the processing of diverse RNA classes. Nucleic Acids Res. 1997 Dec 1;25(23):4778-85. PMID:9365256

[6] Rasmussen TP, Culbertson MR. The putative nucleic acid helicase Sen1p is required for formation and stability of termini and for maximal rates of synthesis and levels of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Dec;18(12):6885-96. PMID:9819377

[7] Zhang Y, Chun Y, Buratowski S, Tong L. Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1. Structure. 2019 Apr 23. pii: S0969-2126(19)30127-3. doi:, 10.1016/j.str.2019.04.005. PMID:31104813 doi:https://dx.doi.org/10.1016/j.str.2019.04.005

[1]

[2]

[3]

[4]

[5]

[6]

[7]

@@ Line 3: / Line 3: @@
 <StructureSection load='6o3w' size='340' side='right'caption='[[6o3w]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6o3w]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O3W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6o3w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O3W FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6o3x|6o3x]], [[6o3y|6o3y]]</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]] 2.1&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NRD1, YNL251C, N0868 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=6o3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o3w OCA], [https://pdbe.org/6o3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o3w RCSB], [https://www.ebi.ac.uk/pdbsum/6o3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o3w ProSAT]</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=6o3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o3w OCA], [http://pdbe.org/6o3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o3w RCSB], [http://www.ebi.ac.uk/pdbsum/6o3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o3w ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SEN1_YEAST SEN1_YEAST]] ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. Directs RNA polymerase II transcription termination on snoRNAs as well as on several short protein-coding genes. May also play a role in transcription-coupled nucleotide excision repair.<ref>PMID:11565036</ref> <ref>PMID:15121901</ref> <ref>PMID:17157256</ref> <ref>PMID:8943355</ref> <ref>PMID:9365256</ref> <ref>PMID:9819377</ref>  [[http://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST]] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.
+[https://www.uniprot.org/uniprot/SEN1_YEAST SEN1_YEAST] ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. Directs RNA polymerase II transcription termination on snoRNAs as well as on several short protein-coding genes. May also play a role in transcription-coupled nucleotide excision repair.<ref>PMID:11565036</ref> <ref>PMID:15121901</ref> <ref>PMID:17157256</ref> <ref>PMID:8943355</ref> <ref>PMID:9365256</ref> <ref>PMID:9819377</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 18: @@
 </div>
 <div class="pdbe-citations 6o3w" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Tong, L]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Zhang, Y]]
+[[Category: Tong L]]
-[[Category: Cid]]
+[[Category: Zhang Y]]
-[[Category: Complex]]
-[[Category: Ctd mimic]]
-[[Category: Hydrolase]]

6o3w: Difference between revisions

Latest revision as of 07:04, 11 October 2023

Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1

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