PDBsum entry 1mky

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protein ligands links
Ligand binding protein PDB id
Protein chain
407 a.a. *
PO4 ×5
Waters ×246
* Residue conservation analysis
PDB id:
Name: Ligand binding protein
Title: Structural analysis of the domain interactions in der, a switch protein containing two gtpase domains
Structure: Probable gtp-binding protein enga. Chain: a. Fragment: two gtpase domains. Engineered: yes. Other_details: probable gtpase
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.90Å     R-factor:   0.204     R-free:   0.224
Authors: V.L.Robinson,J.Hwang,E.Fox,M.Inouye,A.M.Stock
Key ref:
V.L.Robinson et al. (2002). Domain arrangement of Der, a switch protein containing two GTPase domains. Structure, 10, 1649-1658. PubMed id: 12467572 DOI: 10.1016/S0969-2126(02)00905-X
29-Aug-02     Release date:   14-Jan-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9X1F8  (DER_THEMA) -  GTPase Der
439 a.a.
407 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     GTP binding     1 term  


DOI no: 10.1016/S0969-2126(02)00905-X Structure 10:1649-1658 (2002)
PubMed id: 12467572  
Domain arrangement of Der, a switch protein containing two GTPase domains.
V.L.Robinson, J.Hwang, E.Fox, M.Inouye, A.M.Stock.
The EngA subfamily of essential bacterial GTPases has a unique domain structure consisting of two adjacent GTPase domains (GD1 and GD2) and a C-terminal domain. The structure of Thermotoga maritima Der bound to GDP determined at 1.9 A resolution reveals a novel domain arrangement in which the GTPase domains pack at either side of the C-terminal domain. Unexpectedly, the C-terminal domain resembles a KH domain, missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2.
  Selected figure(s)  
Figure 1.
Figure 1. Structure and Topology of TM-Der(A) Stereo Ca trace of a TM-Der monomer, with every 20th residue marked by a black sphere and numbered in blue. Numbers are also indicated for residues flanking regions that are not modeled because of the lack of traceable electron density. The endogenous and substituted methionine residues are indicated as space-filling models and are colored red and green, respectively.(B) The overall fold of the TM-Der protein, with each of the three domains in a different color. GTPase domains 1 and 2 (GD1 and GD2) and the C-terminal domain are colored cyan, green, and yellow, respectively. Residues corresponding to the conserved motifs of the nucleotide binding site in each GTPase domain are colored red. The GDP bound to the second GTPase domain is shown as a red space-filling model. Undefined regions are indicated by dashed lines and correspond to the switch I region of GD1 and the switch I and II regions of GD2. The molecule shown in (B) is rotated approximately 180 about the x axis and 90 about the y axis relative to the orientation shown in (A).
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 1649-1658) copyright 2002.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21354313 R.Lee, M.T.Aung-Htut, C.Kwik, and P.E.March (2011).
Expression phenotypes suggest that Der participates in a specific, high affinity interaction with membranes.
  Protein Expr Purif, 78, 102-112.  
20172997 J.Hwang, and M.Inouye (2010).
Interaction of an essential Escherichia coli GTPase, Der, with the 50S ribosome via the KH-like domain.
  J Bacteriol, 192, 2277-2283.  
20123128 K.W.Hung, Y.W.Chang, E.T.Eng, J.H.Chen, Y.C.Chen, Y.J.Sun, C.D.Hsiao, G.Dong, K.A.Spasov, V.M.Unger, and T.H.Huang (2010).
Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB.
  J Struct Biol, 170, 501-512.
PDB codes: 2wia 2wib 2wic 3k53
19258531 B.A.Maguire (2009).
Inhibition of bacterial ribosome assembly: a suitable drug target?
  Microbiol Mol Biol Rev, 73, 22-35.  
19575570 R.A.Britton (2009).
Role of GTPases in bacterial ribosome assembly.
  Annu Rev Microbiol, 63, 155-176.  
19246542 S.K.Tomar, N.Dhimole, M.Chatterjee, and B.Prakash (2009).
Distinct GDP/GTP bound states of the tandem G-domains of EngA regulate ribosome binding.
  Nucleic Acids Res, 37, 2359-2370.  
18068722 E.T.Eng, A.R.Jalilian, K.A.Spasov, and V.M.Unger (2008).
Characterization of a novel prokaryotic GDP dissociation inhibitor domain from the G protein coupled membrane protein FeoB.
  J Mol Biol, 375, 1086-1097.  
18296517 J.Hwang, and M.Inouye (2008).
RelA functionally suppresses the growth defect caused by a mutation in the G domain of the essential Der protein.
  J Bacteriol, 190, 3236-3243.  
18621905 M.A.deLivron, and V.L.Robinson (2008).
Salmonella enterica serovar Typhimurium BipA exhibits two distinct ribosome binding modes.
  J Bacteriol, 190, 5944-5952.  
17905831 H.K.Lamb, P.Thompson, C.Elliott, I.G.Charles, J.Richards, M.Lockyer, N.Watkins, C.Nichols, D.K.Stammers, C.R.Bagshaw, A.Cooper, and A.R.Hawkins (2007).
Functional analysis of the GTPases EngA and YhbZ encoded by Salmonella typhimurium.
  Protein Sci, 16, 2391-2402.  
17514744 K.Karbstein (2007).
Role of GTPases in ribosome assembly.
  Biopolymers, 87, 1.  
17545283 P.Bachhawat, and A.M.Stock (2007).
Crystal structures of the receiver domain of the response regulator PhoP from Escherichia coli in the absence and presence of the phosphoryl analog beryllofluoride.
  J Bacteriol, 189, 5987-5995.
PDB codes: 2pkx 2pl1
16930151 J.Hwang, and M.Inouye (2006).
The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli.
  Mol Microbiol, 61, 1660-1672.  
16849600 T.A.Hill, J.Broadhvest, R.K.Kuzoff, and C.S.Gasser (2006).
Arabidopsis SHORT INTEGUMENTS 2 is a mitochondrial DAR GTPase.
  Genetics, 174, 707-718.  
16322582 A.Toro-Roman, T.Wu, and A.M.Stock (2005).
A common dimerization interface in bacterial response regulators KdpE and TorR.
  Protein Sci, 14, 3077-3088.
PDB codes: 1zgz 1zh2 1zh4
16333325 E.D.Brown (2005).
Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology.
  Biochem Cell Biol, 83, 738-746.  
16088918 J.Krücken, M.Epe, W.P.Benten, N.Falkenroth, and F.Wunderlich (2005).
Malaria-suppressible expression of the anti-apoptotic triple GTPase mGIMAP8.
  J Cell Biochem, 96, 339-348.  
12732302 C.E.Caldon, and P.E.March (2003).
Function of the universally conserved bacterial GTPases.
  Curr Opin Microbiol, 6, 135-139.  
12753192 K.Inoue, J.Alsina, J.Chen, and M.Inouye (2003).
Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era, an essential GTPase in Escherichia coli.
  Mol Microbiol, 48, 1005-1016.  
12837793 V.L.Robinson, T.Wu, and A.M.Stock (2003).
Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily.
  J Bacteriol, 185, 4186-4194.
PDB code: 1p2f
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