SASDDH9: Chloroplastic phosphoribulokinase (collected using SEC-SAXS)

Basic information

• Entry: Database: SASBDB / ID: SASDDH9

Sample

Chloroplastic phosphoribulokinase (collected using SEC-SAXS)

• Phosphoribulokinase, chloroplastic (protein), CrPRK, Chlamydomonas reinhardtii

Function / homology

Function:

phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / enzyme binding / protein homodimerization activity / ATP binding

Domain/homology:

Phosphoribulokinase signature. / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase

Component:

Phosphoribulokinase, chloroplastic

• Biological species: Chlamydomonas reinhardtii (plant)
• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2019; Title: and phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.; Authors: Libero Gurrieri / Alessandra Del Giudice / Nicola Demitri / Giuseppe Falini / Nicolae Viorel Pavel / Mirko Zaffagnini / Maurizio Polentarutti / Pierre Crozet / Christophe H Marchand / Julien Henri / Paolo Trost / Stéphane D Lemaire / Francesca Sparla / Simona Fermani / ; Abstract: In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga (PRK) and the land plant (PRK). PRK is an elongated homodimer characterized by a large central β-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 Å apart and connected by a flexible region exclusive to photosynthetic eukaryotes-the clamp loop-which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both PRK and PRK have a strongly reduced dimer interface and an increased number of random-coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes.

Contact author

• Alessandra Del Giudice (Sapienza, Sapienza University Rome, Rome, Italy)

Models

• Model #2956: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 0.889; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Chloroplastic phosphoribulokinase (collected using SEC-SAXS)
• Buffer: Name: Tris-HCl 50 mM 150 mM KCl / pH: 7.5

Entity #1177

Name: CrPRK / Type: protein / Description: Phosphoribulokinase, chloroplastic / Formula weight: 38.908 / Num. of mol.: 2 / Source: Chlamydomonas reinhardtii / References: UniProt: P19824
Sequence:

GSHMDKDKTV VIGLAADSGC GKSTFMRRMT SIFGGVPKPP AGGNPDSNTL ISDMTTVICL DDYHCLDRNG RKVKGVTALA PEAQNFDLMY NQVKALKEGK SVDKPIYNHV SGLIDAPEKI ESPPILVIEG LHPFYDKRVA ELLDFKIYLD ISDDIKFAWK IQRDMAERGH SLESIKSSIA ARKPDFDAYI DPQKKDADMI IQVLPTQLVP DDKGQYLRVR LIMKEGSKMF DPVYLFDEGS TISWIPCGRK LTCSFPGIKM FYGPDTWYGQ EVSVLEMDGQ FDKLEELIYV ESHLSNTSAK FYGEITQQML KNSGFPGSNN GTGLFQTIVG LKVREVYERI VKKDVVPV

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.872 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Chloroplastic phosphoribulokinase (collected using SEC-SAXS)
Measurement date: Feb 15, 2016 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 1 sec. / Number of frames: 80 / Unit: 1/nm /

	Min	Max
Q	0.1224	3.5023

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 506 /

	Min	Max
Q	0.12243	2.503
P(R) point	1	506
R	0	11.3

Result

Type of curve: sec
Comments: Additional SEC parameters: Column type: Superdex 200 10/300 GL (GE Healthcare); Flow rate: 0.5 ml/min; Sample injection concentration: 6.1 mg/ml; Injection volume: 100 µl.

	Experimental	Standard	Standard error	Porod
MW	70 kDa	70 kDa	0.2	72 kDa
Volume	-	-	-	115 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	42.42	0.06	42	0.1
Radius of gyration, Rg	3.548 nm	0.008	3.43 nm	0.01

	Min	Max
D	-	11.3
Guinier point	1	55