SASDEE6: Proliferating cell nuclear antigen - SUMOPCNA - Split Fusion Trimer

Basic information

• Entry: Database: SASBDB / ID: SASDEE6

Sample

Proliferating cell nuclear antigen - SUMOPCNA - Split Fusion Trimer

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

Function / homology

Function:

Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / PCNA complex / establishment of mitotic sister chromatid cohesion / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / leading strand elongation / DNA polymerase processivity factor activity / error-free translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / 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 #2533: ; Type: other / Comment: One representative PDB from the simulation. / Chi-square value: 2.581; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Proliferating cell nuclear antigen - SUMOPCNA - Split Fusion Trimer; Specimen concentration: 32.5 mg/ml
• Buffer: Name: 20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP / pH: 7.5 / Comment: 22C

Entity #1329

Name: PCNAProliferating cell nuclear antigen / Type: protein / Description: Proliferating cell nuclear antigen / Formula weight: 41.798 / Num. of mol.: 3
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P15873
Sequence:

MGSSHHHHHH SQDPMSDSEV NQEAKPEVKP EVKPETHINL KVSDGSSEIF FKIKKTTPLR RLMEAFAKRQ GKEMDSLRFL YDGIRIQADQ TPEDLDMEDN DIIEAHREQI GGPGETIKFV ADGDIGSGSV IIKPFVDMEH PETSIKLEMD QPVDLTFGAK YLLDIIKGSS LSDRVGIRLS SEAPALFQFD LKSGFLQFFL APKFNDEEML EAKFEEASLF KRIIDGFKDC VQLVNFQCKE DGIIAQAVDD SRVLLVSLEI GVEAFQEYRC DHPVTLGMDL TSLSKILRCG NNTDTLTLIA DNTPDSIILL FEDTKKDRIA EYSLKLMDID ADFLKIEELQ YDSTLSLPSS EFSKIVRDLS QLSDSINIMI T

Experimental information

• Beam: Instrument name: Advanced Photon Source (APS), Argonne National Laboratory BioCAT 18ID; City: Lemont, IL / 国: USA / Type of source: X-ray synchrotronSynchrotron / 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 - SUMOPCNA - 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: 542 /

	Min	Max
Q	0.00729898	0.171779
P(R) point	1	542
R	0	169.2

Result

Type of curve: sec /

	Experimental	Porod
MW	125.4 kDa	194 kDa
Volume	-	310 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	326.4	324.9	0.5
Radius of gyration, Rg	4.65 nm	4.653 nm	0.08

	Min	Max
D	-	16.92
Guinier point	7	74