SASDED6: Proliferating cell nuclear antigen - UbPCNA - Split Fusion Trimer

Basic information

• Entry: Database: SASBDB / ID: SASDED6

Sample

Proliferating cell nuclear antigen - UbPCNA - Split Fusion Trimer

• Proliferating cell nuclear antigen (protein), PCNA, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Function / homology

Function:

positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / E3 ubiquitin ligases ubiquitinate target proteins / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / Termination of translesion DNA synthesis / PCNA complex / lagging strand elongation / DNA damage tolerance / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / Dual incision in TC-NER / subtelomeric heterochromatin formation / translesion synthesis / mismatch repair / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / nucleotide-excision repair / mitotic cell cycle / chromosome, telomeric region / DNA binding / identical protein binding / nucleus

Domain/homology:

Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / :

Component:

Proliferating cell nuclear antigen

• Biological species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
• Citation: Journal: J Mol Biol / Year: 2018; Title: Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods.; Authors: Kyle T Powers / Emily D Lavering / M Todd Washington / ; Abstract: Ubiquitin-modified proliferating cell nuclear antigen (PCNA) and small ubiquitin-like modifier (SUMO)-modified PCNA regulate DNA damage tolerance pathways. X-ray crystal structures of these proteins suggested that they do not have much conformational flexibility because the modifiers have preferred binding sites on the surface of PCNA. By contrast, small-angle X-ray scattering analyses of these proteins suggested that they have different degrees of conformational flexibility, with SUMO-modified PCNA being more flexible. These conclusions were based on minimal-ensemble hybrid approaches, which produce unrealistic models by representing flexible proteins with only a few static structures. To overcome the limitations of minimal-ensemble hybrid approaches and to determine the degree of conformational flexibility of ubiquitin-modified PCNA and SUMO-modified PCNA, we utilized a novel full-ensemble hybrid approach. We carried out molecular simulations and small-angle X-ray scattering analyses of both proteins and obtained outstanding agreement between the full ensembles generated by the simulations and the experimental data. We found that both proteins have a high degree of conformational flexibility. The modifiers occupy many positions around the back and side of the PCNA ring. Moreover, we found no preferred ubiquitin-binding or SUMO-binding sites on PCNA. This conformational flexibility likely facilitates the recognition of downstream effector proteins and the formation of PCNA tool belts.

Contact author

• Kyle Powers (University of Iowa Carver College of Medicine)

Models

• Model #2532: ; Type: other / Comment: One representative PDB from the simulation. / Chi-square value: 2.650; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Proliferating cell nuclear antigen - UbPCNA - Split Fusion Trimer; Specimen concentration: 20.7 mg/ml
• Buffer: Name: 20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP / pH: 7.5 / Comment: Room temperature

Entity #1328

Name: PCNA / Type: protein / Description: Proliferating cell nuclear antigen / Formula weight: 39.101 / Num. of mol.: 3
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P15873
Sequence:

MGSSHHHHHH SQDPMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGG PGETIKFVAD GDIGSGSVII KPFVDMEHPE TSIKLEMDQP VDLTFGAKYL LDIIKGSSLS DRVGIRLSSE APALFQFDLK SGFLQFFLAP KFNDEEMLEA KFEEASLFKR IIDGFKDCVQ LVNFQCKEDG IIAQAVDDSR VLLVSLEIGV EAFQEYRCDH PVTLGMDLTS LSKILRCGNN TDTLTLIADN TPDSIILLFE DTKKDRIAEY SLKLMDIDAD FLKIEELQYD STLSLPSSEF SKIVRDLSQL SDSINIMIT

Experimental information

• Beam: Instrument name: Advanced Photon Source (APS), Argonne National Laboratory BioCAT 18ID; City: Lemont, IL / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 3.5 mm
• Detector: Name: Pilatus3 X 1M / Pixsize x: 0.172 mm

Scan

Title: Proliferating cell nuclear antigen - UbPCNA - Split Fusion Trimer
Measurement date: Aug 6, 2018 / Storage temperature: 22 °C / Cell temperature: 22 °C / Exposure time: 0.5 sec. / Number of frames: 320 / Unit: 1/A /

	Min	Max
Q	0.0055	0.3857

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 602 /

	Min	Max
Q	0.0103402	0.193046
P(R) point	1	602
R	0	140.3

Result

Type of curve: sec /

	Experimental	Porod
MW	117.3 kDa	148 kDa
Volume	-	238 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	159.9	159.91	0.22
Radius of gyration, Rg	4.14 nm	4.138 nm	0.07

	Min	Max
D	-	14.03
Guinier point	17	86