4jxt: Difference between revisions

Revision as of 11:30, 30 November 2022

CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD

Structural highlights

4jxt is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	BTN, NH2, SEP, UNX
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPR1A_HUMAN Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.^[1] ^[2]

Publication Abstract from PubMed

The RNA polymerase II (RNAPII) C-terminal domain (CTD) heptapeptide repeats (1-YSPTSPS-7) undergo dynamic phosphorylation and dephosphorylation during the transcription cycle to recruit factors that regulate transcription, RNA processing and chromatin modification. We show here that RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains and interact preferentially via CTD-interaction domains (CIDs) with RNAPII CTD repeats phosphorylated at S2 and S7. Crystal structures of the RPRD1A, RPRD1B and RPRD2 CIDs, alone and in complex with RNAPII CTD phosphoisoforms, elucidate the molecular basis of CTD recognition. In an example of cross-talk between different CTD modifications, our data also indicate that RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and, by interacting with CTD repeats where phospho-S2 and/or phospho-S7 bracket a phospho-S5 residue, serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2.

RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.,Ni Z, Xu C, Guo X, Hunter GO, Kuznetsova OV, Tempel W, Marcon E, Zhong G, Guo H, Kuo WH, Li J, Young P, Olsen JB, Wan C, Loppnau P, El Bakkouri M, Senisterra GA, He H, Huang H, Sidhu SS, Emili A, Murphy S, Mosley AL, Arrowsmith CH, Min J, Greenblatt JF Nat Struct Mol Biol. 2014 Jul 6. doi: 10.1038/nsmb.2853. PMID:24997600^[3]

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

References

↑ Liu J, Liu H, Zhang X, Gao P, Wang J, Hu Z. Identification and characterization of P15RS, a novel P15(INK4b) related gene on G1/S progression. Biochem Biophys Res Commun. 2002 Dec 20;299(5):880-5. PMID:12470661
↑ Ni Z, Olsen JB, Guo X, Zhong G, Ruan ED, Marcon E, Young P, Guo H, Li J, Moffat J, Emili A, Greenblatt JF. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. Transcription. 2011 Sep-Oct;2(5):237-42. doi: 10.4161/trns.2.5.17803. PMID:22231121 doi:https://dx.doi.org/10.4161/trns.2.5.17803
↑ Ni Z, Xu C, Guo X, Hunter GO, Kuznetsova OV, Tempel W, Marcon E, Zhong G, Guo H, Kuo WH, Li J, Young P, Olsen JB, Wan C, Loppnau P, El Bakkouri M, Senisterra GA, He H, Huang H, Sidhu SS, Emili A, Murphy S, Mosley AL, Arrowsmith CH, Min J, Greenblatt JF. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Nat Struct Mol Biol. 2014 Jul 6. doi: 10.1038/nsmb.2853. PMID:24997600 doi:https://dx.doi.org/10.1038/nsmb.2853

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Liu J, Liu H, Zhang X, Gao P, Wang J, Hu Z. Identification and characterization of P15RS, a novel P15(INK4b) related gene on G1/S progression. Biochem Biophys Res Commun. 2002 Dec 20;299(5):880-5. PMID:12470661

[2] Ni Z, Olsen JB, Guo X, Zhong G, Ruan ED, Marcon E, Young P, Guo H, Li J, Moffat J, Emili A, Greenblatt JF. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. Transcription. 2011 Sep-Oct;2(5):237-42. doi: 10.4161/trns.2.5.17803. PMID:22231121 doi:https://dx.doi.org/10.4161/trns.2.5.17803

[3] Ni Z, Xu C, Guo X, Hunter GO, Kuznetsova OV, Tempel W, Marcon E, Zhong G, Guo H, Kuo WH, Li J, Young P, Olsen JB, Wan C, Loppnau P, El Bakkouri M, Senisterra GA, He H, Huang H, Sidhu SS, Emili A, Murphy S, Mosley AL, Arrowsmith CH, Min J, Greenblatt JF. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Nat Struct Mol Biol. 2014 Jul 6. doi: 10.1038/nsmb.2853. PMID:24997600 doi:https://dx.doi.org/10.1038/nsmb.2853

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD==
-<StructureSection load='4jxt' size='340' side='right' caption='[[4jxt]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='4jxt' size='340' side='right'caption='[[4jxt]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4jxt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JXT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4jxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JXT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></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=4jxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jxt OCA], [https://pdbe.org/4jxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jxt RCSB], [https://www.ebi.ac.uk/pdbsum/4jxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jxt ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPRD1A, P15RS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4jxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jxt OCA], [http://pdbe.org/4jxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jxt RCSB], [http://www.ebi.ac.uk/pdbsum/4jxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jxt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPR1A_HUMAN RPR1A_HUMAN]] Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.<ref>PMID:12470661</ref> <ref>PMID:22231121</ref>  [[http://www.uniprot.org/uniprot/RPB1_HUMAN RPB1_HUMAN]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Acts as a RNA-dependent RNA polymerase when associated with small delta antigen of Hepatitis delta virus, acting both as a replicate and transcriptase for the viral RNA circular genome.<ref>PMID:9852112</ref> <ref>PMID:18032511</ref>
+[https://www.uniprot.org/uniprot/RPR1A_HUMAN RPR1A_HUMAN] Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.<ref>PMID:12470661</ref> <ref>PMID:22231121</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H]]
+[[Category: Large Structures]]
-[[Category: Bakkouri, M El]]
+[[Category: Arrowsmith CH]]
-[[Category: Bountra, C]]
+[[Category: Bountra C]]
-[[Category: Edwards, A M]]
+[[Category: Edwards AM]]
-[[Category: Greenblatt, J F]]
+[[Category: El Bakkouri M]]
-[[Category: Guo, X]]
+[[Category: Greenblatt JF]]
-[[Category: Loppnau, P]]
+[[Category: Guo X]]
-[[Category: Min, J]]
+[[Category: Loppnau P]]
-[[Category: Ni, Z]]
+[[Category: Min J]]
-[[Category: Structural genomic]]
+[[Category: Ni Z]]
-[[Category: Tempel, W]]
+[[Category: Tempel W]]
-[[Category: Weigelt, J]]
+[[Category: Weigelt J]]
-[[Category: Xu, C]]
+[[Category: Xu C]]
-[[Category: Protein binding]]
-[[Category: Sgc]]

4jxt: Difference between revisions

Revision as of 11:30, 30 November 2022

CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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