spacer
spacer

PDBsum entry 2d6f
Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Ligase/RNA PDB id
2d6f

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
424 a.a. *
485 a.a. *
522 a.a. *
DNA/RNA
Metals
_ZN ×2
Waters ×180
* Residue conservation analysis
PDB id:
2d6f
Name: Ligase/RNA
Title: Crystal structure of glu-tRNA(gln) amidotransferase in the complex with tRNA(gln)
Structure: tRNA. Chain: e, f. Engineered: yes. Glutamyl-tRNA(gln) amidotransferase subunit d. Chain: a, b. Synonym: gatd, glu-adt subunit d. Engineered: yes. Glutamyl-tRNA(gln) amidotransferase subunit e. Chain: c, d.
Source: Synthetic: yes. Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
3.15Å     R-factor:   0.230     R-free:   0.292
Authors: O.Nureki
Key ref:
H.Oshikane et al. (2006). Structural basis of RNA-dependent recruitment of glutamine to the genetic code. Science, 312, 1950-1954. PubMed id: 16809540 DOI: 10.1126/science.1128470
Date:
13-Nov-05     Release date:   11-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O26802  (GATD_METTH) -  Glutamyl-tRNA(Gln) amidotransferase subunit D from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Seq:
Struc: 		435 a.a.
424 a.a.
Protein chain
Pfam   ArchSchema ?
O26803  (GATE_METTH) -  Glutamyl-tRNA(Gln) amidotransferase subunit E from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Seq:
Struc: 		 
Seq:
Struc: 		619 a.a.
485 a.a.
Protein chain
Pfam   ArchSchema ?
O26803  (GATE_METTH) -  Glutamyl-tRNA(Gln) amidotransferase subunit E from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Seq:
Struc: 		 
Seq:
Struc: 		619 a.a.
522 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-G-U-C-C-C-G-U-G-G-G-G-U-A-G-U-G-G-U-A-A-U-C-C-U-G-C-U-G-G-G-C-U-U-U-G-G-A-C- 72 bases
  A-G-U-C-C-C-G-U-G-G-G-G-U-A-G-U-G-G-U-A-A-U-C-C-U-G-C-U-G-G-G-C-U-U-U-G-G-A-C- 74 bases

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.6.3.5.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1126/science.1128470 Science 312:1950-1954 (2006)
PubMed id: 16809540  
 
 
Structural basis of RNA-dependent recruitment of glutamine to the genetic code.
H.Oshikane, K.Sheppard, S.Fukai, Y.Nakamura, R.Ishitani, T.Numata, R.L.Sherrer, L.Feng, E.Schmitt, M.Panvert, S.Blanquet, Y.Mechulam, D.Söll, O.Nureki.
 
  ABSTRACT  
 
Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overall structure of the 1:1 complex of GatDE and tRNA^Gln[1] (molecules B, D, and F). The protein domains are colored differently; in GatD, the N-terminal domain, AnsA-like domain 1, and AnsA-like domain 2 are shown in light green, blue, and red, respectively; whereas in GatE, the AspRS-like insertion domain, cradle domain, helical domain, and Yqey-like tail domain are colored violet, cyan, orange, and pink, respectively. In the present structure, the Yqey-like tail domain is shown as translucent because its side chains are disordered, despite the fact that the main chain was traced in the electron density map. The bound tRNA molecules are yellow. In GatE, His15, Glu157, and Glu184, which coordinate to an essential Mg2+ ion (red), are shown to highlight the Glu-tRNA^Gln kinase and amidotransferase sites. Gln240, which recognizes A73 (red), and Asp463, which recognizes G52 (red), are indicated. All figures of the molecular models were prepared with the program CueMol (www.cuemol.org/). 		Figure 4.
Fig. 4. Ternary complex formation between GatE, GluRS, and tRNA^Gln. Docking of T. thermophilus GluRS complexed with tRNA^Glu (29) onto the present GatE·tRNA^Gln complex was accomplished by superposing the complexed tRNA structures. In GatDE, the AspRS-like insertion domain, cradle domain, helical domain, and tail domain are colored violet, cyan, orange, and pink, respectively. GluRS and tRNA are shown in gray and yellow, respectively.
 
  The above figures are reprinted by permission from the AAAs: Science (2006, 312, 1950-1954) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19906721 A.Nakamura, K.Sheppard, J.Yamane, M.Yao, D.Söll, and I.Tanaka (2010).
Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition.
  Nucleic Acids Res, 38, 672-682.
PDB code: 3ip4
  20871851 B.de Koning, F.Blombach, S.J.Brouns, and J.van der Oost (2010).
Fidelity in archaeal information processing.
  Archaea, 2010, 0.  
20717102 M.Blaise, M.Bailly, M.Frechin, M.A.Behrens, F.Fischer, C.L.Oliveira, H.D.Becker, J.S.Pedersen, S.Thirup, and D.Kern (2010).
Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.
  EMBO J, 29, 3118-3129.
PDB code: 3kfu
19903480 R.Banerjee, S.Chen, K.Dare, M.Gilreath, M.Praetorius-Ibba, M.Raina, N.M.Reynolds, T.Rogers, H.Roy, S.S.Yadavalli, and M.Ibba (2010).
tRNAs: cellular barcodes for amino acids.
  FEBS Lett, 584, 387-395.  
20882017 T.Ito, and S.Yokoyama (2010).
Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.
  Nature, 467, 612-616.
PDB codes: 3akz 3al0
20457752 T.Rampias, K.Sheppard, and D.Söll (2010).
The archaeal transamidosome for RNA-dependent glutamine biosynthesis.
  Nucleic Acids Res, 38, 5774-5783.  
19043064 A.L.Menon, F.L.Poole, A.Cvetkovic, S.A.Trauger, E.Kalisiak, J.W.Scott, S.Shanmukh, J.Praissman, F.E.Jenney, W.R.Wikoff, J.V.Apon, G.Siuzdak, and M.W.Adams (2009).
Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome.
  Mol Cell Proteomics, 8, 735-751.  
19805282 A.Nagao, T.Suzuki, T.Katoh, Y.Sakaguchi, and T.Suzuki (2009).
Biogenesis of glutaminyl-mt tRNAGln in human mitochondria.
  Proc Natl Acad Sci U S A, 106, 16209-16214.  
19520089 J.Wu, W.Bu, K.Sheppard, M.Kitabatake, S.T.Kwon, D.Söll, and J.L.Smith (2009).
Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme.
  J Mol Biol, 391, 703-716.
PDB codes: 3h0l 3h0m 3h0r
19755501 K.M.Chang, and T.L.Hendrickson (2009).
Recognition of tRNAGln by Helicobacter pylori GluRS2--a tRNAGln-specific glutamyl-tRNA synthetase.
  Nucleic Acids Res, 37, 6942-6949.  
19720833 M.A.Khan, W.E.Walden, D.J.Goss, and E.C.Theil (2009).
Direct Fe2+ sensing by iron-responsive messenger RNA:repressor complexes weakens binding.
  J Biol Chem, 284, 30122-30128.  
19805283 Y.Araiso, R.L.Sherrer, R.Ishitani, J.M.Ho, D.Söll, and O.Nureki (2009).
Structure of a tRNA-dependent kinase essential for selenocysteine decoding.
  Proc Natl Acad Sci U S A, 106, 16215-16220.
PDB codes: 3a4l 3a4m 3a4n
18522650 C.D.Hausmann, and M.Ibba (2008).
Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed.
  FEMS Microbiol Rev, 32, 705-721.  
18425141 C.M.Zhang, C.Liu, S.Slater, and Y.M.Hou (2008).
Aminoacylation of tRNA with phosphoserine for synthesis of cysteinyl-tRNA(Cys).
  Nat Struct Mol Biol, 15, 507-514.  
18604446 J.Yuan, K.Sheppard, and D.Söll (2008).
Amino acid modifications on tRNA.
  Acta Biochim Biophys Sin (Shanghai), 40, 539-553.  
18279892 K.Sheppard, and D.Söll (2008).
On the evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE.
  J Mol Biol, 377, 831-844.  
18252769 K.Sheppard, J.Yuan, M.J.Hohn, B.Jester, K.M.Devine, and D.Söll (2008).
From one amino acid to another: tRNA-dependent amino acid biosynthesis.
  Nucleic Acids Res, 36, 1813-1825.  
18241795 K.Sheppard, P.M.Akochy, and D.Söll (2008).
Assays for transfer RNA-dependent amino acid biosynthesis.
  Methods, 44, 139-145.  
18291416 K.Sheppard, R.L.Sherrer, and D.Söll (2008).
Methanothermobacter thermautotrophicus tRNA Gln confines the amidotransferase GatCAB to asparaginyl-tRNA Asn formation.
  J Mol Biol, 377, 845-853.  
18267971 R.L.Sherrer, J.M.Ho, and D.Söll (2008).
Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase.
  Nucleic Acids Res, 36, 1871-1880.  
18174226 R.L.Sherrer, P.O'Donoghue, and D.Söll (2008).
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation.
  Nucleic Acids Res, 36, 1247-1259.  
18158303 Y.Araiso, S.Palioura, R.Ishitani, R.L.Sherrer, P.O'Donoghue, J.Yuan, H.Oshikane, N.Domae, J.Defranco, D.Söll, and O.Nureki (2008).
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation.
  Nucleic Acids Res, 36, 1187-1199.
PDB code: 2z67
17580114 H.Li (2007).
Complexes of tRNA and maturation enzymes: shaping up for translation.
  Curr Opin Struct Biol, 17, 293-301.  
17964262 M.Bailly, M.Blaise, B.Lorber, H.D.Becker, and D.Kern (2007).
The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis.
  Mol Cell, 28, 228-239.  
17284460 M.Deniziak, C.Sauter, H.D.Becker, C.A.Paulus, R.Giegé, and D.Kern (2007).
Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation.
  Nucleic Acids Res, 35, 1421-1431.
PDB code: 2hz7
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
17214986 S.Namgoong, K.Sheppard, R.L.Sherrer, and D.Söll (2007).
Co-evolution of the archaeal tRNA-dependent amidotransferase GatCAB with tRNA(Asn).
  FEBS Lett, 581, 309-314.  
17533454 T.Cathopoulis, P.Chuawong, and T.L.Hendrickson (2007).
Novel tRNA aminoacylation mechanisms.
  Mol Biosyst, 3, 408-418.  
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.

 

spacer
spacer