6eht

From Proteopedia

(Difference between revisions)

Revision as of 06:36, 22 August 2018

Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme

Structural highlights

6eht is a 7 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	PCNA (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PCNA_HUMAN] Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion.^[1] ^[2] [PAF15_HUMAN] PCNA-binding protein that acts as a regulator of DNA repair during DNA replication. Following DNA damage, the interaction with PCNA is disrupted, facilitating the interaction between monoubiquitinated PCNA and the translesion DNA synthesis DNA polymerase eta (POLH) at stalled replisomes, facilitating the bypass of replication-fork-blocking lesions. Also acts as a regulator of centrosome number.^[3] ^[4]

Publication Abstract from PubMed

p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF-PCNA-DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol delta). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol eta). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol eta-PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.

p15PAF binding to PCNA modulates the DNA sliding surface.,De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magana A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A Nucleic Acids Res. 2018 Aug 8. pii: 5068262. doi: 10.1093/nar/gky723. PMID:30102405^[5]

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

References

↑ Burkovics P, Hajdu I, Szukacsov V, Unk I, Haracska L. Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'-5' exonuclease activities of human Ape2 in repair of oxidative DNA damage. Nucleic Acids Res. 2009 Jul;37(13):4247-55. doi: 10.1093/nar/gkp357. Epub 2009, May 13. PMID:19443450 doi:10.1093/nar/gkp357
↑ Motegi A, Liaw HJ, Lee KY, Roest HP, Maas A, Wu X, Moinova H, Markowitz SD, Ding H, Hoeijmakers JH, Myung K. Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks. Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12411-6. Epub 2008 Aug 21. PMID:18719106 doi:0805685105
↑ Kais Z, Barsky SH, Mathsyaraja H, Zha A, Ransburgh DJ, He G, Pilarski RT, Shapiro CL, Huang K, Parvin JD. KIAA0101 interacts with BRCA1 and regulates centrosome number. Mol Cancer Res. 2011 Aug;9(8):1091-9. doi: 10.1158/1541-7786.MCR-10-0503. Epub, 2011 Jun 14. PMID:21673012 doi:http://dx.doi.org/10.1158/1541-7786.MCR-10-0503
↑ Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. Nat Cell Biol. 2012 Oct;14(10):1089-98. doi: 10.1038/ncb2579. Epub 2012 Sep 23. PMID:23000965 doi:http://dx.doi.org/10.1038/ncb2579
↑ De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magana A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A. p15PAF binding to PCNA modulates the DNA sliding surface. Nucleic Acids Res. 2018 Aug 8. pii: 5068262. doi: 10.1093/nar/gky723. PMID:30102405 doi:http://dx.doi.org/10.1093/nar/gky723

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6eht"

@@ Line 3: / Line 3: @@
 <StructureSection load='6eht' size='340' side='right' caption='[[6eht]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6eht]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EHT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EHT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6eht]] is a 7 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=6EHT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EHT FirstGlance]. <br>
-</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=6eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eht OCA], [http://pdbe.org/6eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eht RCSB], [http://www.ebi.ac.uk/pdbsum/6eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eht ProSAT]</span></td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PCNA ([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=6eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eht OCA], [http://pdbe.org/6eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eht RCSB], [http://www.ebi.ac.uk/pdbsum/6eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eht ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 10: / Line 11: @@
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-The intrinsically disordered protein p15(PAF) regulates DNA replication and repair by binding to the proliferating cell nuclear antigen (PCNA) sliding clamp. We present the structure of the human p15(PAF)-PCNA complex. Crystallography and NMR show the central PCNA-interacting protein motif (PIP-box) of p15(PAF) tightly bound to the front-face of PCNA. In contrast to other PCNA-interacting proteins, p15(PAF) also contacts the inside of, and passes through, the PCNA ring. The disordered p15(PAF) termini emerge at opposite faces of the ring, but remain protected from 20S proteasomal degradation. Both free and PCNA-bound p15(PAF) binds DNA mainly through its histone-like N-terminal tail, while PCNA does not, and a model of the ternary complex with DNA inside the PCNA ring is consistent with electron micrographs. We propose that p15(PAF) acts as a flexible drag that regulates PCNA sliding along the DNA and facilitates the switch from replicative to translesion synthesis polymerase binding.
+p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF-PCNA-DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol delta). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol eta). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol eta-PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.
-Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair.,De Biasio A, de Opakua AI, Mortuza GB, Molina R, Cordeiro TN, Castillo F, Villate M, Merino N, Delgado S, Gil-Carton D, Luque I, Diercks T, Bernado P, Montoya G, Blanco FJ Nat Commun. 2015 Mar 12;6:6439. doi: 10.1038/ncomms7439. PMID:25762514<ref>PMID:25762514</ref>
+p15PAF binding to PCNA modulates the DNA sliding surface.,De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magana A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A Nucleic Acids Res. 2018 Aug 8. pii: 5068262. doi: 10.1093/nar/gky723. PMID:30102405<ref>PMID:30102405</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Barrera-Vilarmau, S]]
 [[Category: Biasio, A De]]

6eht

From Proteopedia

Revision as of 06:36, 22 August 2018

Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox