SASDCE2: Rab family protein CtRoco L487A GDP (Rab family protein, CtRoco)

Basic information

Entry

Database: SASBDB / ID: SASDCE2

Sample

Rab family protein CtRoco L487A GDP

• Rab family protein (protein), CtRoco, Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)

Function / homology

Function:

GTP binding / identical protein binding

Domain/homology:

C-terminal of Roc (COR) domain / C-terminal of Roc, COR, domain / Ras of Complex, Roc, domain of DAPkinase / Leucine rich repeat, ribonuclease inhibitor type / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Roc domain profile. / Roc domain / Leucine Rich repeat / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Rab subfamily of small GTPases / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase

Component:

Rab family protein

• Biological species: Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
• Citation: Journal: Nat Commun / Year: 2017; Title: A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.; Authors: Egon Deyaert / Lina Wauters / Giambattista Guaitoli / Albert Konijnenberg / Margaux Leemans / Susanne Terheyden / Arsen Petrovic / Rodrigo Gallardo / Laura M Nederveen-Schippers / Panagiotis S Athanasopoulos / Henderikus Pots / Peter J M Van Haastert / Frank Sobott / Christian Johannes Gloeckner / Rouslan Efremov / Arjan Kortholt / Wim Versées / ; Abstract: Mutations in LRRK2 are a common cause of genetic Parkinson's disease (PD). LRRK2 is a multi-domain Roco protein, harbouring kinase and GTPase activity. In analogy with a bacterial homologue, LRRK2 was proposed to act as a GTPase activated by dimerization (GAD), while recent reports suggest LRRK2 to exist under a monomeric and dimeric form in vivo. It is however unknown how LRRK2 oligomerization is regulated. Here, we show that oligomerization of a homologous bacterial Roco protein depends on the nucleotide load. The protein is mainly dimeric in the nucleotide-free and GDP-bound states, while it forms monomers upon GTP binding, leading to a monomer-dimer cycle during GTP hydrolysis. An analogue of a PD-associated mutation stabilizes the dimer and decreases the GTPase activity. This work thus provides insights into the conformational cycle of Roco proteins and suggests a link between oligomerization and disease-associated mutations in LRRK2.

Contact author

• Egon Deyaert (VUB, Vrije Universiteit Brussel, Pleinlaan 2 1050 Brussel)

Models

Sample

• Sample: Name: Rab family protein CtRoco L487A GDP / Specimen concentration: 1.00-2.00
• Buffer: Name: 20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT 200µM GDP; pH: 7.5

Entity #601

Name: CtRoco / Type: protein / Description: Rab family protein / Formula weight: 127.147 / Num. of mol.: 2
Source: Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
References: UniProt: Q8KC98
Sequence:

MSYYHHHHHH DYDIPTTENL YFQGAMGSMS DLDVIRQIEQ ELGMQLEPVD KLKWYSKGYK LDKDQRVTAI GLYDCGSDTL DRIIQPLESL KSLSELSLSS NQITDISPLA SLNSLSMLWL DRNQITDIAP LASLNSLSML WLFGNKISDI APLESLKSLT ELQLSSNQIT DIAPLASLKS LTELSLSGNN ISDIAPLESL KSLTELSLSS NQITDIAPLA SLKSLTELSL SSNQISDIAP LESLKSLTEL QLSRNQISDI APLESLKSLT ELQLSSNQIT DIAPLASLKS LTELQLSRNQ ISDIAPLESL NSLSKLWLNG NQITDIAPLA SLNSLTELEL SSNQITDIAP LASLKSLSTL WLSSNQISDI APLASLESLS ELSLSSNQIS DISPLASLNS LTGFDVRRNP IKRLPETITG FDMEILWNDF SSSGFITFFD NPLESPPPEI VKQGKEAVRQ YFQSIEEARS KGEALVHLQE IKVHLIGDGM AGKTSLLKQL IGETFDPKES QTHGLNVVTK QAPNIKGLEN DDELKECLFH FWDFGGQEIM HASHQFFMTR SSVYMLLLDS RTDSNKHYWL RHIEKYGGKS PVIVVMNKID ENPSYNIEQK KINERFPAIE NRFHRISCKN GDGVESIAKS LKSAVLHPDS IYGTPLAPSW IKVKEKLVEA TTAQRYLNRT EVEKICNDSG ITDPGERKTL LGYLNNLGIV LYFEALDLSE IYVLDPHWVT IGVYRIINSS KTKNGHLNTS ALGYILNEEQ IRCDEYDPAK NNKFTYTLLE QRYLLDIMKQ FELCYDEGKG LFIIPSNLPT QIDNEPEITE GEPLRFIMKY DYLPSTIIPR LMIAMQHQIL DRMQWRYGMV LKSQDHEGAL AKVVAETKDS TITIAIQGEP RCKREYLSII WYEIKKINAN FTNLDVKEFI PLPGHPDELV EYKELLGLEK MGRDEYVSGK LEKVFSVSKM LDSVISKEER NKERLMGDIN IKLENIGNPT IPIHQQVEVN VSQETVQHVE NLQGFFENLK ADILREAELE IDDPKERKRL ANELELAENA ITKMDAAVKS GKNKLKPDVK DRLGEFIDNL ANENSRLRKG IALVMNGAEK VQKLARYYNN VAPFFDLPSV PPVLLGKEKT

Experimental information

• Beam: Instrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.103 Å
• Detector: Name: AVIEX / Type: CCD

Scan

Title: Rab family protein CtRoco L487A GDP / Measurement date: Jun 17, 2015 / Cell temperature: 25 °C / Exposure time: 0.75 sec. / Number of frames: 36 / Unit: 1/A /

	Min	Max
Q	0.0061	0.5535

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 260 /

	Min	Max
Q	0.007654	0.1398
P(R) point	1	260
R	0	218

Result

Type of curve: other /

	Experimental	Porod
MW	257 kDa	276 kDa
Volume	-	469.21 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.1363	3.0E-5	0.1355	5.0E-5
Radius of gyration, Rg	6.04 nm	0.003	5.87 nm	0.004

	Min	Max
D	-	21.8
Guinier point	4	27