SASDAH4: DH-PH (DH-PH module of PDZRhoGEF)

Basic information

• Entry: Database: SASBDB / ID: SASDAH4

Sample

DH-PH

• DH-PH module of PDZRhoGEF (protein), DH-PH, Homo sapiens

• Biological species: Homo sapiens (human)
• Citation: Journal: Protein Sci / Year: 2009; Title: The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoA.; Authors: Tomasz Cierpicki / Jakub Bielnicki / Meiying Zheng / Jakub Gruszczyk / Marta Kasterka / Maxim Petoukhov / Aming Zhang / Erik J Fernandez / Dmitri I Svergun / Urszula Derewenda / John H Bushweller / Zygmunt S Derewenda / ; Abstract: The DH-PH domain tandems of Dbl-homology guanine nucleotide exchange factors catalyze the exchange of GTP for GDP in Rho-family GTPases, and thus initiate a wide variety of cellular signaling cascades. Although several crystal structures of complexes of DH-PH tandems with cognate, nucleotide free Rho GTPases are known, they provide limited information about the dynamics of the complex and it is not clear how accurately they represent the structures in solution. We used a complementary combination of nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and hydrogen-deuterium exchange mass spectrometry (DXMS) to study the solution structure and dynamics of the DH-PH tandem of RhoA-specific exchange factor PDZRhoGEF, both in isolation and in complex with nucleotide free RhoA. We show that in solution the DH-PH tandem behaves as a rigid entity and that the mutual disposition of the DH and PH domains remains identical within experimental error to that seen in the crystal structure of the complex, thus validating the latter as an accurate model of the complex in vivo. We also show that the nucleotide-free RhoA exhibits elevated dynamics when in complex with DH-PH, a phenomenon not observed in the crystal structure, presumably due to the restraining effects of crystal contacts. The complex is readily and rapidly dissociated in the presence of both GDP and GTP nucleotides, with no evidence of intermediate ternary complexes.

Contact author

• Maxim Petoukhov (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #61: ; Type: dummy / Software: Dammin / Radius of dummy atoms: 1.90 A / Chi-square value: 2.458624; Search similar-shape structures of this assembly by Omokage search (details)
• Model #62: ; Type: atomic / Software: Crysol / Chi-square value: 2.399401; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: DH-PH / Sample MW: 41 kDa / Specimen concentration: 0.86-4.70
• Buffer: Name: 50 mM Tris-HCL / pH: 7.5 / Composition: 150 mM NaCl, 1.0 mM DTT

Entity #57

Name: DH-PH / Type: protein / Description: DH-PH module of PDZRhoGEF / Formula weight: 41 / Num. of mol.: 1 / Source: Homo sapiens
Sequence:

QNWQHTVGKD VVAGLTQREI DRQEVINELF VTEASHLRTL RVLDLIFYQR MKKENLMPRE ELARLFPNLP ELIEIHNSWC EAMKKLREEG PIIKEISDLM LARFDGPARE ELQQVAAQFC SYQSIALELI KTKQRKESRF QLFMQEAESH PQCRRLQLRD LIISEMQRLT KYPLLLESII KHTEGGTSEH EKLCRARDQC REILKYVNEA VKQTENRHRL EGYQKRLDAT ALERASNPLA AEFKSLDLTT RKMIHEGPLT WRISKDKTLD LHVLLLEDLL VLLQKQDEKL LLKCTFSPVL KLNAVLIRSV ATDKRAFFII CTSKLGPPQI YELVALTSSD KNTWMELLEE AVRNA

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron
• Detector: Name: MAR 345 Image Plate

Scan

Title: DH-PH / Measurement date: Oct 30, 2008 / Storage temperature: 10 °C / Cell temperature: 10 °C / Unit: 1/nm /

	Min	Max
Q	0.2295	4.816

Distance distribution function P(R)

Sofotware P(R): GNOM 4.5a / Number of points: 369 /

	Min	Max
Q	0.2571	2.796
P(R) point	12	380
R	0	8.941

Result

I0 from Guinier: 0.378 / Rg from Guinier: 2.9 nm / Type of curve: merged / Standard: BSA /

	Experimental	Porod
MW	40 kDa	-
Volume	-	60 nm3

/

	Min	Max
D	-	9
Guinier point	1	96