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PDBsum entry 1a2b

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protein ligands metals links
Oncogene protein PDB id
1a2b
Jmol
Contents
Protein chain
178 a.a. *
Ligands
GSP
Metals
_MG
Waters ×38
* Residue conservation analysis
PDB id:
1a2b
Name: Oncogene protein
Title: Human rhoa complexed with gtp analogue
Structure: Transforming protein rhoa. Chain: a. Fragment: residues 1 - 181. Engineered: yes. Mutation: yes. Other_details: complexed with one gtpgammas and one mg ion
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
2.40Å     R-factor:   0.195     R-free:   0.268
Authors: K.Ihara,S.Muraguchi,M.Kato,T.Shimizu,M.Shirakawa,S.Kuroda, K.Kaibuchi,T.Hakoshima
Key ref:
K.Ihara et al. (1998). Crystal structure of human RhoA in a dominantly active form complexed with a GTP analogue. J Biol Chem, 273, 9656-9666. PubMed id: 9545299 DOI: 10.1074/jbc.273.16.9656
Date:
26-Dec-97     Release date:   17-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61586  (RHOA_HUMAN) -  Transforming protein RhoA
Seq:
Struc:
193 a.a.
178 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   15 terms 
  Biological process     viral reproduction   34 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
DOI no: 10.1074/jbc.273.16.9656 J Biol Chem 273:9656-9666 (1998)
PubMed id: 9545299  
 
 
Crystal structure of human RhoA in a dominantly active form complexed with a GTP analogue.
K.Ihara, S.Muraguchi, M.Kato, T.Shimizu, M.Shirakawa, S.Kuroda, K.Kaibuchi, T.Hakoshima.
 
  ABSTRACT  
 
The 2.4-A resolution crystal structure of a dominantly active form of the small guanosine triphosphatase (GTPase) RhoA, RhoAV14, complexed with the nonhydrolyzable GTP analogue, guanosine 5'-3-O-(thio)triphosphate (GTPgammaS), reveals a fold similar to RhoA-GDP, which has been recently reported (Wei, Y., Zhang, Y., Derewenda, U., Liu, X., Minor, W., Nakamoto, R. K., Somlyo, A. V., Somlyo, A. P., and Derewenda, Z. S. (1997) Nat. Struct. Biol. 4, 699-703), but shows large conformational differences localized in switch I and switch II. These changes produce hydrophobic patches on the molecular surface of switch I, which has been suggested to be involved in its effector binding. Compared with H-Ras and other GTPases bound to GTP or GTP analogues, the significant conformational differences are located in regions involving switches I and II and part of the antiparallel beta-sheet between switches I and II. Key residues that produce these conformational differences were identified. In addition to these differences, RhoA contains four insertion or deletion sites with an extra helical subdomain that seems to be characteristic of members of the Rho family, including Rac1, but with several variations in details. These sites also display large displacements from those of H-Ras. The ADP-ribosylation residue, Asn41, by C3-like exoenzymes stacks on the indole ring of Trp58 with a hydrogen bond to the main chain of Glu40. The recognition of the guanosine moiety of GTPgammaS by the GTPase contains water-mediated hydrogen bonds, which seem to be common in the Rho family. These structural differences provide an insight into specific interaction sites with the effectors, as well as with modulators such as guanine nucleotide exchange factor (GEF) and guanine nucleotide dissociation inhibitor (GDI).
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. GTP S bound to RhoA^V14. A cartoon of GTP S binding to RhoA^V14 with Mg2+ and water molecules. All dashed lines correspond to hydrogen bonding interactions (distance less than 3.5 Å), and the corresponding distances (Å) are indicated. The residues whose main chains participate in the hydrogen bonding are represented by rectangles, and the residues whose side chains participate in the hydrogen bonding are represented by ovals. The coordination bonds to the Mg2+ ion are indicated by arrows. The possible hydrogen bond between Gln63 and Wat-3 has a longer distance (3.8 Å). The hydrogen bonds observed in the current structure but not in H-Ras are highlighted in red.
Figure 6.
Fig. 6. Molecular surface of RhoA^V14. Residues whose mutations abolish the interaction with GEF are in yellow. Asn41 is also highlighted in green. Switches I and II are shown in red and blue, respectively. This surface also contains most of the residues corresponding to the effector-binding residues as seen in the complex between the Ras-binding domain of Raf1 and a double mutant Rap1A (E30D/K31E), which mimics Ras.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 9656-9666) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20649471 J.Heo (2011).
Redox control of GTPases: from molecular mechanisms to functional significance in health and disease.
  Antioxid Redox Signal, 14, 689-724.  
  21492154 V.Zazueta-Novoa, G.Martínez-Cadena, G.M.Wessel, R.Zazueta-Sandoval, L.Castellano, and J.García-Soto (2011).
Concordance and interaction of guanine nucleotide dissociation inhibitor (RhoGDI) with RhoA in oogenesis and early development of the sea urchin.
  Dev Growth Differ, 53, 427-439.  
20236512 M.Della Peruta, C.Giagulli, C.Laudanna, A.Scarpa, and C.Sorio (2010).
RHOA and PRKCZ control different aspects of cell motility in pancreatic cancer metastatic clones.
  Mol Cancer, 9, 61.  
20062059 M.Yamashita, K.Kurokawa, Y.Sato, A.Yamagata, H.Mimura, A.Yoshikawa, K.Sato, A.Nakano, and S.Fukai (2010).
Structural basis for the Rho- and phosphoinositide-dependent localization of the exocyst subunit Sec3.
  Nat Struct Mol Biol, 17, 180-186.
PDB code: 3a58
20980621 N.Zhang, J.Liang, Y.Tian, L.Yuan, L.Wu, S.Miao, S.Zong, and L.Wang (2010).
A novel testis-specific GTPase serves as a link to proteasome biogenesis: functional characterization of RhoS/RSA-14-44 in spermatogenesis.
  Mol Biol Cell, 21, 4312-4324.  
19460155 M.Zheng, T.Cierpicki, K.Momotani, M.V.Artamonov, U.Derewenda, J.H.Bushweller, A.V.Somlyo, and Z.S.Derewenda (2009).
On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF.
  BMC Struct Biol, 9, 36.  
18946488 D.Komander, R.Garg, P.T.Wan, A.J.Ridley, and D.Barford (2008).
Mechanism of multi-site phosphorylation from a ROCK-I:RhoE complex structure.
  EMBO J, 27, 3175-3185.
PDB code: 2v55
18348980 M.J.Phillips, G.Calero, B.Chan, S.Ramachandran, and R.A.Cerione (2008).
Effector proteins exert an important influence on the signaling-active state of the small GTPase Cdc42.
  J Biol Chem, 283, 14153-14164.
PDB code: 2qrz
18393397 M.Soundararajan, A.Turnbull, O.Fedorov, C.Johansson, and D.A.Doyle (2008).
RhoB can adopt a Mg2+ free conformation prior to GEF binding.
  Proteins, 72, 498-505.  
17622352 C.L.Reyes, E.Rutenber, P.Walter, and R.M.Stroud (2007).
X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates.
  PLoS ONE, 2, e607.
PDB codes: 2q9a 2q9b 2q9c
17201675 G.W.Feigenson (2007).
Phase boundaries and biological membranes.
  Annu Rev Biophys Biomol Struct, 36, 63-77.  
17146673 M.Vogelsgesang, A.Pautsch, and K.Aktories (2007).
C3 exoenzymes, novel insights into structure and action of Rho-ADP-ribosylating toxins.
  Naunyn Schmiedebergs Arch Pharmacol, 374, 347-360.  
17468740 S.Gras, V.Chaumont, B.Fernandez, P.Carpentier, F.Charrier-Savournin, S.Schmitt, C.Pineau, D.Flament, A.Hecker, P.Forterre, J.Armengaud, and D.Housset (2007).
Structural insights into a new homodimeric self-activated GTPase family.
  EMBO Rep, 8, 569-575.
PDB codes: 1yr6 1yr7 1yr8 1yr9 1yra 1yrb 2oxr
16751107 A.F.Roth, J.Wan, A.O.Bailey, B.Sun, J.A.Kuchar, W.N.Green, B.S.Phinney, J.R.Yates, and N.G.Davis (2006).
Global analysis of protein palmitoylation in yeast.
  Cell, 125, 1003-1013.  
16866878 A.Yanuar, S.Sakurai, K.Kitano, and T.Hakoshima (2006).
Crystal structure of human Rad GTPase of the RGK-family.
  Genes Cells, 11, 961-968.
PDB code: 2dpx
15831824 D.E.Voth, and J.D.Ballard (2005).
Clostridium difficile toxins: mechanism of action and role in disease.
  Clin Microbiol Rev, 18, 247-263.  
16246732 L.Hemsath, R.Dvorsky, D.Fiegen, M.F.Carlier, and M.R.Ahmadian (2005).
An electrostatic steering mechanism of Cdc42 recognition by Wiskott-Aldrich syndrome proteins.
  Mol Cell, 20, 313-324.
PDB code: 2atx
15563612 Q.Zhong, J.Gvozdenovic-Jeremic, P.Webster, J.Zhou, and M.L.Greenberg (2005).
Loss of function of KRE5 suppresses temperature sensitivity of mutants lacking mitochondrial anionic lipids.
  Mol Biol Cell, 16, 665-675.  
15577926 R.Dvorsky, and M.R.Ahmadian (2004).
Always look on the bright site of Rho: structural implications for a conserved intermolecular interface.
  EMBO Rep, 5, 1130-1136.  
12777804 K.Longenecker, P.Read, S.K.Lin, A.P.Somlyo, R.K.Nakamoto, and Z.S.Derewenda (2003).
Structure of a constitutively activated RhoA mutant (Q63L) at 1.55 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 876-880.
PDB code: 1kmq
12773565 K.Riento, R.M.Guasch, R.Garg, B.Jin, and A.J.Ridley (2003).
RhoE binds to ROCK I and inhibits downstream signaling.
  Mol Cell Biol, 23, 4219-4229.  
12847085 M.Abe, H.Qadota, A.Hirata, and Y.Ohya (2003).
Lack of GTP-bound Rho1p in secretory vesicles of Saccharomyces cerevisiae.
  J Cell Biol, 162, 85-97.  
14556626 M.Geyer, C.Wilde, J.Selzer, K.Aktories, and H.R.Kalbitzer (2003).
Glucosylation of Ras by Clostridium sordellii lethal toxin: consequences for effector loop conformations observed by NMR spectroscopy.
  Biochemistry, 42, 11951-11959.  
14576104 P.J.Budge, J.Lebowitz, and B.S.Graham (2003).
Antiviral activity of RhoA-derived peptides against respiratory syncytial virus is dependent on formation of peptide dimers.
  Antimicrob Agents Chemother, 47, 3470-3477.  
11814347 C.Wilde, I.Just, and K.Aktories (2002).
Structure-function analysis of the Rho-ADP-ribosylating exoenzyme C3stau2 from Staphylococcus aureus.
  Biochemistry, 41, 1539-1544.  
12068804 D.H.Roh, B.Bowers, H.Riezman, and E.Cabib (2002).
Rho1p mutations specific for regulation of beta(1-->3)glucan synthesis and the order of assembly of the yeast cell wall.
  Mol Microbiol, 44, 1167-1183.  
12009891 H.Garavini, K.Riento, J.P.Phelan, M.S.McAlister, A.J.Ridley, and N.H.Keep (2002).
Crystal structure of the core domain of RhoE/Rnd3: a constitutively activated small G protein.
  Biochemistry, 41, 6303-6310.
PDB code: 1gwn
11900529 R.Thapar, A.E.Karnoub, and S.L.Campbell (2002).
Structural and biophysical insights into the role of the insert region in Rac1 function.
  Biochemistry, 41, 3875-3883.  
11809807 X.Li, X.Bu, B.Lu, H.Avraham, R.A.Flavell, and B.Lim (2002).
The hematopoiesis-specific GTP-binding protein RhoH is GTPase deficient and modulates activities of other Rho GTPases by an inhibitory function.
  Mol Cell Biol, 22, 1158-1171.  
11283263 A.E.Karnoub, C.J.Der, and S.L.Campbell (2001).
The insert region of Rac1 is essential for membrane ruffling but not cellular transformation.
  Mol Cell Biol, 21, 2847-2857.  
11687661 A.G.Spencer, S.Orita, C.J.Malone, and M.Han (2001).
A RHO GTPase-mediated pathway is required during P cell migration in Caenorhabditis elegans.
  Proc Natl Acad Sci U S A, 98, 13132-13137.  
11222756 F.Rivero, H.Dislich, G.Glöckner, and A.A.Noegel (2001).
The Dictyostelium discoideum family of Rho-related proteins.
  Nucleic Acids Res, 29, 1068-1079.  
11463812 H.Zong, K.Kaibuchi, and L.A.Quilliam (2001).
The insert region of RhoA is essential for Rho kinase activation and cellular transformation.
  Mol Cell Biol, 21, 5287-5298.  
11566135 S.Padmanabhan, and D.M.Freymann (2001).
The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.
  Structure, 9, 859-867.
PDB codes: 1jpj 1jpn
11258916 Z.Zhu, J.J.Dumas, S.E.Lietzke, and D.G.Lambright (2001).
A helical turn motif in Mss4 is a critical determinant of Rab binding and nucleotide release.
  Biochemistry, 40, 3027-3036.
PDB code: 1hxr
10970849 B.Prakash, L.Renault, G.J.Praefcke, C.Herrmann, and A.Wittinghofer (2000).
Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.
  EMBO J, 19, 4555-4564.
PDB code: 1f5n
11042449 C.Busch, and K.Aktories (2000).
Microbial toxins and the glycosylation of rho family GTPases.
  Curr Opin Struct Biol, 10, 528-535.  
10676816 G.R.Hoffman, N.Nassar, and R.A.Cerione (2000).
Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI.
  Cell, 100, 345-356.
PDB code: 1doa
  10716190 P.W.Read, X.Liu, K.Longenecker, C.G.Dipierro, L.A.Walker, A.V.Somlyo, A.P.Somlyo, and R.K.Nakamoto (2000).
Human RhoA/RhoGDI complex expressed in yeast: GTP exchange is sufficient for translocation of RhoA to liposomes.
  Protein Sci, 9, 376-386.  
10737920 T.Uno, A.Nakasuji, W.Hara, and Y.Aizono (2000).
Molecular cloning of a cDNA for a small GTP binding protein, BRho, from the embryo of Bombyx mori and its characterization after expression and purification.
  Arch Insect Biochem Physiol, 43, 165-172.  
10367892 I.R.Vetter, A.Arndt, U.Kutay, D.Görlich, and A.Wittinghofer (1999).
Structural view of the Ran-Importin beta interaction at 2.3 A resolution.
  Cell, 97, 635-646.
PDB code: 1ibr
10591105 J.Ménétrey, and J.Cherfils (1999).
Structure of the small G protein Rap2 in a non-catalytic complex with GTP.
  Proteins, 37, 465-473.
PDB code: 3rap
10489445 K.Longenecker, P.Read, U.Derewenda, Z.Dauter, X.Liu, S.Garrard, L.Walker, A.V.Somlyo, R.K.Nakamoto, A.P.Somlyo, and Z.S.Derewenda (1999).
How RhoGDI binds Rho.
  Acta Crystallogr D Biol Crystallogr, 55, 1503-1515.
PDB code: 1cc0
  10211824 M.G.Rudolph, A.Wittinghofer, and I.R.Vetter (1999).
Nucleotide binding to the G12V-mutant of Cdc42 investigated by X-ray diffraction and fluorescence spectroscopy: two different nucleotide states in one crystal.
  Protein Sci, 8, 778-787.
PDB code: 1a4r
  10438814 M.K.Pastey, J.E.Crowe, and B.S.Graham (1999).
RhoA interacts with the fusion glycoprotein of respiratory syncytial virus and facilitates virus-induced syncytium formation.
  J Virol, 73, 7262-7270.  
10619026 R.Maesaki, K.Ihara, T.Shimizu, S.Kuroda, K.Kaibuchi, and T.Hakoshima (1999).
The structural basis of Rho effector recognition revealed by the crystal structure of human RhoA complexed with the effector domain of PKN/PRK1.
  Mol Cell, 4, 793-803.
PDB code: 1cxz
10583404 S.Müller, C.von Eichel-Streiber, and M.Moos (1999).
Impact of amino acids 22-27 of Rho-subfamily GTPases on glucosylation by the large clostridial cytotoxins TcsL-1522, TcdB-1470 and TcdB-8864.
  Eur J Biochem, 266, 1073-1080.  
10462759 V.Benard, G.M.Bokoch, and B.A.Diebold (1999).
Potential drug targets: small GTPases that regulate leukocyte function.
  Trends Pharmacol Sci, 20, 365-370.  
10384329 R.Treisman, A.S.Alberts, and E.Sahai (1998).
Regulation of SRF activity by Rho family GTPases.
  Cold Spring Harb Symp Quant Biol, 63, 643-651.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.