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PDBsum entry 2gj9

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2gj9
Jmol
Contents
Protein chains
161 a.a. *
Ligands
ALF ×4
GDP ×4
Metals
_MG ×4
_RB ×4
Waters ×14
* Residue conservation analysis
PDB id:
2gj9
Name: Hydrolase
Title: Structure of the mnme g-domain in complex with gdp Alf4-, mg2+ and rb+
Structure: tRNA modification gtpase trme. Chain: a, b, c, d. Fragment: g-domain (216-g384). Synonym: mnme. Engineered: yes
Source: Escherichia coli bl21(de3). Organism_taxid: 469008. Strain: bl21de3. Gene: trme, mnme, thdf. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.252     R-free:   0.299
Authors: A.Scrima,A.Wittinghofer
Key ref:
A.Scrima and A.Wittinghofer (2006). Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element. EMBO J, 25, 2940-2951. PubMed id: 16763562 DOI: 10.1038/sj.emboj.7601171
Date:
30-Mar-06     Release date:   04-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P25522  (MNME_ECOLI) -  tRNA modification GTPase MnmE
Seq:
Struc:
454 a.a.
161 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     small GTPase mediated signal transduction   1 term 
  Biochemical function     GTP binding     1 term  

 

 
DOI no: 10.1038/sj.emboj.7601171 EMBO J 25:2940-2951 (2006)
PubMed id: 16763562  
 
 
Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element.
A.Scrima, A.Wittinghofer.
 
  ABSTRACT  
 
MnmE, a Guanine nucleotide-binding protein conserved between bacteria and man, is involved in the modification of tRNAs. Here we provide biochemical and X-ray structural evidence for a new GTP-hydrolysis mechanism, where the G-domains of MnmE dimerise in a potassium-dependent manner and induce GTP hydrolysis. The structure in the presence of GDP-AlFx and potassium shows how juxtaposition of the subunits induces a conformational change around the nucleotide which reorients the catalytic machinery. A critical glutamate is positioned such as to stabilise or activate the attacking water. Potassium provides a positive charge into the catalytic site in a position analogous to the arginine finger in the Ras-RasGAP system. Mutational studies show that potassium-dependent dimerisation and GTP hydrolysis can be uncoupled and that interaction between the G-domains is a prerequisite for subsequent phosphoryl transfer. We propose a model for the juxtaposition of G-domains in the full-length protein and how it induces conformational changes in the putative tRNA-modification centre.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 MnmE G-domain dimer structure. (A) Ribbon presentation of the MnmE G-domain dimer (G216–G384), with molecules A and B in green and cyan, respectively, with switch I and II (yellow), P-loop (red) and K-loop (purple) highlighted, and GDP, AlF[4]^-, Mg^2+ and K^+ as ball-and-stick models. (B) Stereo view of the superimposition of the nucleotide-free and GDP-AlF[x]-bound structures of the G-domain, highlighting potassium-induced conformational changes in helix G 2, the switches and G 4 (purple), which is converted into a -strand G [con] (blue).
Figure 4.
Figure 4 Nucleotide binding and catalysis. (A) Schematic representation of the binding site of GDP-AlF[4]^- and potassium. (B) The catalytic centre as viewed from the in-line attacking water towards AlF[4]^-. The K-loop together with the phosphates, the AlF[4]^- and Asn226 coordinates the potassium ion and shields it from the surrounding solvent. The three positive charges of the P-loop Lys229, Mg^2+ and K^+ form a triangle around what represents the -bridging oxygen of GTP. (C) Structural analysis with RbCl. The anomalous density (contoured at 2 ) of the Rb^+ position is shown in red, the 2F[O]-F[C] map surrounding the GDP-AlF[x] and Mg^2+ (contoured at 2 ) in green. (D) Superimposition of the Ras-RasGAP (Ras: blue; RasGAP: green) structure and the GDP-AlF[4]^--bound G-domain (cyan). Red and yellow water molecules belong to MnmE and Ras-RasGAP, respectively. Note the close juxtaposition of the Gln61 side-chain oxygen and the bridging water (b.w.) from MnmE, and the superimposition of the guanidinium group from the Arg-finger (Arg789) of RasGAP and the potassium ion from MnmE.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 2940-2951) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21276251 N.Pawlowski, A.Khaminets, J.P.Hunn, N.Papic, A.Schmidt, R.C.Uthaiah, R.Lange, G.Vopper, S.Martens, E.Wolf, and J.C.Howard (2011).
The activation mechanism of Irga6, an interferon-inducible GTPase contributing to mouse resistance against Toxoplasma gondii.
  BMC Biol, 9, 7.  
20376346 B.Anand, P.Surana, and B.Prakash (2010).
Deciphering the catalytic machinery in 30S ribosome assembly GTPase YqeH.
  PLoS One, 5, e9944.  
20186121 B.Sot, C.Kötting, D.Deaconescu, Y.Suveyzdis, K.Gerwert, and A.Wittinghofer (2010).
Unravelling the mechanism of dual-specificity GAPs.
  EMBO J, 29, 1205-1214.  
20498089 E.M.Shepard, S.E.McGlynn, A.L.Bueling, C.S.Grady-Smith, S.J.George, M.A.Winslow, S.P.Cramer, J.W.Peters, and J.B.Broderick (2010).
Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold.
  Proc Natl Acad Sci U S A, 107, 10448-10453.  
20428113 J.S.Chappie, S.Acharya, M.Leonard, S.L.Schmid, and F.Dyda (2010).
G domain dimerization controls dynamin's assembly-stimulated GTPase activity.
  Nature, 465, 435-440.
PDB codes: 2x2e 2x2f
20957720 N.Pawlowski (2010).
Dynamin self-assembly and the vesicle scission mechanism: how dynamin oligomers cleave the membrane neck of clathrin-coated pits during endocytosis.
  Bioessays, 32, 1033-1039.  
19767610 I.Moukadiri, S.Prado, J.Piera, A.Velázquez-Campoy, G.R.Björk, and M.E.Armengod (2009).
Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions.
  Nucleic Acids Res, 37, 7177-7193.  
19033377 K.H.Nielsen, H.Chamieh, C.B.Andersen, F.Fredslund, K.Hamborg, H.Le Hir, and G.R.Andersen (2009).
Mechanism of ATP turnover inhibition in the EJC.
  RNA, 15, 67-75.
PDB code: 3ex7
19805342 M.Sirajuddin, M.Farkasovsky, E.Zent, and A.Wittinghofer (2009).
GTP-induced conformational changes in septins and implications for function.
  Proc Natl Acad Sci U S A, 106, 16592-16597.
PDB code: 3ftq
19424291 R.Gasper, S.Meyer, K.Gotthardt, M.Sirajuddin, and A.Wittinghofer (2009).
It takes two to tango: regulation of G proteins by dimerization.
  Nat Rev Mol Cell Biol, 10, 423-429.  
19806182 S.Meyer, S.Böhme, A.Krüger, H.J.Steinhoff, J.P.Klare, and A.Wittinghofer (2009).
Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy.
  PLoS Biol, 7, e1000212.
PDB codes: 3gee 3geh 3gei
  19052377 A.Priyadarshi, K.H.Nam, E.E.Kim, and K.Y.Hwang (2008).
Crystallization and preliminary X-ray crystallographic analysis of the probable tRNA-modification GTPase (TrmE) from Staphylococcus aureus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1166-1168.  
18309292 A.Scrima, C.Thomas, D.Deaconescu, and A.Wittinghofer (2008).
The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues.
  EMBO J, 27, 1145-1153.
PDB code: 3brw
18478031 C.S.Weirich, J.P.Erzberger, and Y.Barral (2008).
The septin family of GTPases: architecture and dynamics.
  Nat Rev Mol Cell Biol, 9, 478-489.  
18772884 J.P.Hunn, S.Koenen-Waisman, N.Papic, N.Schroeder, N.Pawlowski, R.Lange, F.Kaiser, J.Zerrahn, S.Martens, and J.C.Howard (2008).
Regulatory interactions between IRG resistance GTPases in the cellular response to Toxoplasma gondii.
  EMBO J, 27, 2495-2509.  
18650931 K.Gotthardt, M.Weyand, A.Kortholt, P.J.Van Haastert, and A.Wittinghofer (2008).
Structure of the Roc-COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase.
  EMBO J, 27, 2239-2249.
PDB codes: 3dpt 3dpu
18801746 M.Moreau, G.I.Lee, Y.Wang, B.R.Crane, and D.F.Klessig (2008).
AtNOS/AtNOA1 Is a Functional Arabidopsis thaliana cGTPase and Not a Nitric-oxide Synthase.
  J Biol Chem, 283, 32957-32967.  
18186482 M.Roovers, Y.Oudjama, K.H.Kaminska, E.Purta, J.Caillet, L.Droogmans, and J.M.Bujnicki (2008).
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
  Proteins, 71, 2076-2085.  
18852288 M.Villarroya, S.Prado, J.M.Esteve, M.A.Soriano, C.Aguado, D.Pérez-Martínez, J.I.Martínez-Ferrandis, L.Yim, V.M.Victor, E.Cebolla, A.Montaner, E.Knecht, and M.E.Armengod (2008).
Characterization of human GTPBP3, a GTP-binding protein involved in mitochondrial tRNA modification.
  Mol Cell Biol, 28, 7514-7531.  
18400179 P.Koenig, M.Oreb, A.Höfle, S.Kaltofen, K.Rippe, I.Sinning, E.Schleiff, and I.Tews (2008).
The GTPase cycle of the chloroplast import receptors Toc33/Toc34: implications from monomeric and dimeric structures.
  Structure, 16, 585-596.
PDB codes: 3bb1 3bb3 3bb4
18541539 P.Koenig, M.Oreb, K.Rippe, C.Muhle-Goll, I.Sinning, E.Schleiff, and I.Tews (2008).
On the significance of Toc-GTPase homodimers.
  J Biol Chem, 283, 23104-23112.
PDB code: 3def
17261809 D.Barillà, E.Carmelo, and F.Hayes (2007).
The tail of the ParG DNA segregation protein remodels ParF polymers and enhances ATP hydrolysis via an arginine finger-like motif.
  Proc Natl Acad Sci U S A, 104, 1811-1816.  
17184999 J.Gawronski-Salerno, and D.M.Freymann (2007).
Structure of the GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY.
  J Struct Biol, 158, 122-128.
PDB code: 2j7p
17637674 M.Sirajuddin, M.Farkasovsky, F.Hauer, D.Kühlmann, I.G.Macara, M.Weyand, H.Stark, and A.Wittinghofer (2007).
Structural insight into filament formation by mammalian septins.
  Nature, 449, 311-315.
PDB codes: 2qa5 2qag
17337454 Y.H.Yeh, M.M.Kesavulu, H.M.Li, S.Z.Wu, Y.J.Sun, E.H.Konozy, and C.D.Hsiao (2007).
Dimerization is important for the GTPase activity of chloroplast translocon components atToc33 and psToc159.
  J Biol Chem, 282, 13845-13853.
PDB code: 2j3e
17052716 Y.Opatowsky, Y.Sasson, I.Shaked, Y.Ward, O.Chomsky-Hecht, Y.Litvak, Z.Selinger, K.Kelly, and J.A.Hirsch (2006).
Structure-function studies of the G-domain from human gem, a novel small G-protein.
  FEBS Lett, 580, 5959-5964.
PDB code: 2ht6
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 codes are shown on the right.