PDBsum entry 1ow3

Gene regulation/signaling protein

PDB id: 1ow3

Contents

Protein chains

196 a.a. *

179 a.a. *

Ligands

GDP-MGF

Metals

_MG

Waters ×374

* Residue conservation analysis

PDB id:

1ow3

Name:

Gene regulation/signaling protein

Title:

Crystal structure of rhoa.Gdp.Mgf3-in complex with rhogap

Structure:

Rho-gtpase-activating protein 1. Chain: a. Synonym: gtpase-activating protein rhoogap, rho-related small gtpase protein activator, cdc42 gtpase-activating protein, p50-rhogap. Engineered: yes. Transforming protein rhoa. Chain: b. Synonym: h12. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rhogap1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rhoa. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.188 R-free: 0.219

Authors:

D.L.Graham,P.N.Lowe,G.W.Grime,M.Marsh,K.Rittinger,S.J.Smerdon, S.J.Gamblin,J.F.Eccleston

Key ref:

D.L.Graham et al. (2002). MgF(3)(-) as a transition state analog of phosphoryl transfer. Chem Biol, 9, 375-381. PubMed id: 11927263 DOI: 10.1016/S1074-5521(02)00112-6

Date:

28-Mar-03 Release date: 06-May-03

Protein chain

Q07960  (RHG01_HUMAN) -  Rho GTPase-activating protein 1 from Homo sapiens

Seq: 439 a.a.

Struc: 196 a.a.

Protein chain

P61586  (RHOA_HUMAN) -  Transforming protein RhoA from Homo sapiens

Seq: 193 a.a.

Struc: 179 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.?
• Enzyme class 3: Chain B: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/S1074-5521(02)00112-6

Chem Biol 9:375-381 (2002)

PubMed id: 11927263

MgF(3)(-) as a transition state analog of phosphoryl transfer.

D.L.Graham, P.N.Lowe, G.W.Grime, M.Marsh, K.Rittinger, S.J.Smerdon, S.J.Gamblin, J.F.Eccleston.

ABSTRACT

The formation of complexes between small G proteins and certain of their effectors can be facilitated by aluminum fluorides. Solution studies suggest that magnesium may be able to replace aluminum in such complexes. We have determined the crystal structure of RhoA.GDP bound to RhoGAP in the presence of Mg(2+) and F(-) but without Al(3+). The metallofluoride adopts a trigonal planar arrangement instead of the square planar structure of AlF(4)(-). We have confirmed that these crystals contain magnesium and not aluminum by proton-induced X-ray emission spectroscopy. The structure adopted by GDP.MgF(-) possesses the stereochemistry and approximate charge expected for the transition state. We suggest that MgF3(-) may be the reagent of choice for studying phosphoryl transfer reactions.

Selected figure(s)

Figure 1.
Figure 1. Crystal Structures of Rho/RhoGAP Complex(A) shows the complex between the catalytic GAP domain of p50RhoGAP (α helices shown as blue cylinders) and the Mg.GDP.MgF[3]^− (shown as yellow ball and stick) complex of RhoA (α helices as red cylinders and β strands in green). The catalytic arginine residue (R85) from the GAP domain is shown in green interacting with the metallo-fluoride moiety. The overall arrangements of the two proteins and the interactions made at their interface are very similar to those previously described for the complex of RhoA.Mg.GDP.AlF[4]^−/RhoGAP [13]. The figure was produced with the program Ribbons [29].(B) The top and bottom panels show electron density maps for the “AlF[4]^−” and “MgF[3]^−” complexes, respectively, together with a ball-and-stick representation for the catalytic R85 from RhoGAP, the GDP, and the metallo-fluoride moiety. The electron density maps were calculated with (Fo − Fc) coefficients where the amplitudes and phases were calculated from the atomic model with the coordinates for R85 and the metallo-fluoride omitted from the last cycles of refinement.(C) The top panel shows, in ball-and-stick representation, molecular details of the active site of the complex with “AlF[4]^−” while the bottom panels show the same view for the complex with “MgF[3]^−.” Arg 85 from RhoGAP is colored yellow while the residues from RhoA are shown in gray. The GDP and metallo-fluoride moiety are shown in magenta while water molecules are in green. The distances for the various interactions shown are presented in Table 3. The interactions of Lys18 and Gly62 of Rho with the metallo-fluoride moiety have been omitted from this figure (but not 2B and 2C) for clarity.

The above figure is reprinted by permission from Cell Press: Chem Biol (2002, 9, 375-381) copyright 2002.