SASDD22: Glyceraldehyde-3-phosphate dehydrogenase in complex with oxidised...

Basic information

Entry

Database: SASBDB / ID: SASDD22

Sample

Glyceraldehyde-3-phosphate dehydrogenase in complex with oxidised chloroplastic calvin cycle protein CP12 (C. reinhardtii)Glyceraldehyde 3-phosphate dehydrogenase

• Calvin cycle protein CP12, chloroplastic (protein), CP12, Chlamydomonas reinhardtii
• Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase (protein), GAPDHGlyceraldehyde 3-phosphate dehydrogenase, Chlamydomonas reinhardtii

Function / homology

Function:

negative regulation of reductive pentose-phosphate cycle / supramolecular complex / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / reductive pentose-phosphate cycle / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / nickel cation binding / chloroplast / positive regulation of protein-containing complex assembly / glucose metabolic process / NAD binding / NADP binding / molecular adaptor activity / lyase activity / copper ion binding / enzyme binding / protein-containing complex

Domain/homology:

Calvin cycle protein CP12-like / CP12 domain / CP12 / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily

Component:

Calvin cycle protein CP12, chloroplastic / Glyceraldehyde-3-phosphate dehydrogenase

• Biological species: Chlamydomonas reinhardtii (plant)
• Citation: Journal: J Mol Biol / Year: 2018; Title: Cryptic Disorder Out of Disorder: Encounter between Conditionally Disordered CP12 and Glyceraldehyde-3-Phosphate Dehydrogenase.; Authors: Hélène Launay / Patrick Barré / Carine Puppo / Yizhi Zhang / Stéphanie Maneville / Brigitte Gontero / Véronique Receveur-Bréchot / ; Abstract: Among intrinsically disordered proteins, conditionally disordered proteins undergo dramatic structural disorder rearrangements upon environmental changes and/or post-translational modifications that directly modulate their function. Quantifying the dynamics of these fluctuating proteins is extremely challenging but paramount to understanding the regulation of their function. The chloroplast protein CP12 is a model of such proteins and acts as a redox switch by formation/disruption of its two disulfide bridges. It regulates the Calvin cycle by forming, in oxidized conditions, a supramolecular complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and then phosphoribulokinase. In this complex, both enzymes are inactive. The highly dynamic nature of CP12 has so far hindered structural characterization explaining its mode of action. Thanks to a synergistic combination of small-angle X-ray scattering, nuclear magnetic resonance and circular dichroism that drove the molecular modeling of structural ensembles, we deciphered the structural behavior of Chlamydomonas reinhardtii oxidized CP12 alone and in the presence of GAPDH. Contrary to sequence-based structural predictions, the N-terminal region is unstable, oscillates at the ms timescale between helical and random conformations, and is connected through a disordered linker to its C-terminus, which forms a stable helical turn. Upon binding to GAPDH, oxidized CP12 undergoes an induced unfolding of its N-terminus. This phenomenon called cryptic disorder contributes to decrease the entropy cost and explains CP12 unusual high affinity for its partners.

Contact author

• Veronique Receveur-Brechot (Aix Marseille Univ, CNRS, BIP UMR7281, Marseille, France)

Models

Sample

• Sample: Name: Glyceraldehyde-3-phosphate dehydrogenase in complex with oxidised chloroplastic calvin cycle protein CP12 (C. reinhardtii)Glyceraldehyde 3-phosphate dehydrogenase; Specimen concentration: 16 mg/ml / Entity id: 907 / 911
• Buffer: Name: 30 mM Tris, 4 mM EDTA, 100 µM NAD, 5 mM free cysteine; pH: 7.9

Entity #907

Name: CP12 / Type: protein / Description: Calvin cycle protein CP12, chloroplastic / Formula weight: 10.934 / Num. of mol.: 1 / Source: Chlamydomonas reinhardtii / References: UniProt: A6Q0K5
Sequence:

HHHHHHHHHH SSGHIEGRHM SGQPAVDLNK KVQDAVKEAE DACAKGTSAD CAVAWDTVEE LSAAVSHKKD AVKADVTLTD PLEAFCKDAP DADECRVYED

Entity #911

Name: GAPDHGlyceraldehyde 3-phosphate dehydrogenase / Type: protein
Description: Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
Formula weight: 36.881 / Num. of mol.: 4 / Source: Chlamydomonas reinhardtii / References: UniProt: A8HP84
Sequence:

EKKIRVAING FGRIGRNFLR CWHGRQNTLL DVVAINDSGG VKQASHLLKY DSTLGTFAAD VKIVDDSHIS VDGKQIKIVS SRDPLQLPWK EMNIDLVIEG TGVFIDKVGA GKHIQAGASK VLITAPAKDK DIPTFVVGVN EGDYKHEYPI ISNASCTTNC LAPFVKVLEQ KFGIVKGTMT TTHSYTGDQR LLDASHRDLR RARAAALNIV PTTTGAAKAV SLVLPSLKGK LNGIALRVPT PTVSVVDLVV QVEKKTFAEE VNAAFREAAN GPMKGVLHVE DAPLVSIDFK CTDQSTSIDA SLTMVMGDDM VKVVAWYDNE WGYSQRVVDL AEVTAKKWVA

Experimental information

• Beam: Instrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 1.832 mm
• Detector: Name: AVIEX / Type: CCD

Scan

Title: Glyceraldehyde-3-phosphate dehydrogenase in complex with oxidised chloroplastic calvin cycle protein CP12 (C. reinhardtii)
Measurement date: Dec 8, 2010 / Storage temperature: 15 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 250 / Unit: 1/A /

	Min	Max
Q	0.0105	0.4595

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 407 /

	Min	Max
Q	0.01081	0.4595
P(R) point	1	407
R	0	190

Result

Type of curve: sec /

	Experimental	Porod
MW	166 kDa	-
Volume	-	250.82 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.0003877	2.0E-7	0.0003852	1.0E-8
Radius of gyration, Rg	3.99 nm	0.006	3.84 nm	0.01

	Min	Max	Error
D	-	19	1
Guinier point	1	31	-