PDBsum entry 1dpf

Gene regulation/signaling protein

PDB id: 1dpf

Contents

Protein chain

178 a.a. *

Ligands

GDP

Waters ×187

* Residue conservation analysis

PDB id:

1dpf

Name:

Gene regulation/signaling protein

Title:

Crystal structure of a mg-free form of rhoa complexed with gdp

Structure:

Rhoa. Chain: a. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.201 R-free: 0.252

Authors:

T.Shimizu,K.Ihara,R.Maesaki,S.Kuroda,K.Kaibuchi,T.Hakoshima

Key ref:

T.Shimizu et al. (2000). An open conformation of switch I revealed by the crystal structure of a Mg2+-free form of RHOA complexed with GDP. Implications for the GDP/GTP exchange mechanism. J Biol Chem, 275, 18311-18317. PubMed id: 10748207 DOI: 10.1074/jbc.M910274199

Date:

27-Dec-99 Release date: 21-Jun-00

Protein chain

P61586  (RHOA_HUMAN) -  Transforming protein RhoA from Homo sapiens

Seq: 193 a.a.

Struc: 178 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M910274199

J Biol Chem 275:18311-18317 (2000)

PubMed id: 10748207

An open conformation of switch I revealed by the crystal structure of a Mg2+-free form of RHOA complexed with GDP. Implications for the GDP/GTP exchange mechanism.

T.Shimizu, K.Ihara, R.Maesaki, S.Kuroda, K.Kaibuchi, T.Hakoshima.

ABSTRACT

Mg(2+) ions are essential for guanosine triphosphatase (GTPase) activity and play key roles in guanine nucleotide binding and preserving the structural integrity of GTP-binding proteins. We determined the crystal structure of a small GTPase RHOA complexed with GDP in the absence of Mg(2+) at 2.0-A resolution. Elimination of a Mg(2+) ion induces significant conformational changes in the switch I region that opens up the nucleotide-binding site. Similar structural changes have been observed in the switch regions of Ha-Ras bound to its guanine nucleotide exchange factor, Sos. This RHOA-GDP structure reveals an important regulatory role for Mg(2+) and suggests that guanine nucleotide exchange factor may utilize this feature of switch I to produce an open conformation in GDP/GTP exchange.

Selected figure(s)

Figure 5.
Fig. 5. A diagram showing the coordination of GDP in the RHOA Mg2+-free form. All dashed lines correspond to hydrogen bonding interactions (distance less than 3.5 Å), and the corresponding distances are indicated. The hydrogen bonds observed in the current structure but not in the GDP/Mg2+-bound form are highlighted in red.

Figure 6.
Fig. 6. Summary of contacts of the RHOA Mg2+-free form around the switch I region. Thin and thick dashed lines correspond to hydrogen bonding and van der Waals interactions, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 18311-18317) copyright 2000.

Figures were selected by an automated process.