spacer
spacer

PDBsum entry 2g5h
Go to PDB code: 
protein metals Protein-protein interface(s) links
Ligase PDB id
2g5h

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
485 a.a. *
398 a.a. *
99 a.a. *
Metals
_MG
Waters ×139
* Residue conservation analysis
PDB id:
2g5h
Name: Ligase
Title: Structure of tRNA-dependent amidotransferase gatcab
Structure: Glutamyl-tRNA(gln) amidotransferase subunit a. Chain: a. Synonym: glu-adt subunit a. Engineered: yes. Aspartyl/glutamyl-tRNA(asn/gln) amidotransferase subunit b. Chain: b. Synonym: asp/glu-adt subunit b. Engineered: yes. Aspartyl/glutamyl-tRNA(asn/gln) amidotransferase subunit c.
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: mu50. Gene: gata. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: gatb. Gene: gatc.
Biol. unit: Trimer (from PQS)
Resolution:
2.50Å     R-factor:   0.238     R-free:   0.275
Authors: A.Nakamura,M.Yao,I.Tanaka
Key ref:
A.Nakamura et al. (2006). Ammonia channel couples glutaminase with transamidase reactions in GatCAB. Science, 312, 1954-1958. PubMed id: 16809541 DOI: 10.1126/science.1127156
Date:
23-Feb-06     Release date:   18-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P63488  (GATA_STAAM) -  Glutamyl-tRNA(Gln) amidotransferase subunit A from Staphylococcus aureus (strain Mu50 / ATCC 700699)
Seq:
Struc: 		485 a.a.
485 a.a.
Protein chain
Pfam   ArchSchema ?
P64201  (GATB_STAAM) -  Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B from Staphylococcus aureus (strain Mu50 / ATCC 700699)
Seq:
Struc: 		475 a.a.
398 a.a.
Protein chain
Pfam   ArchSchema ?
P68807  (GATC_STAAM) -  Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C from Staphylococcus aureus (strain Mu50 / ATCC 700699)
Seq:
Struc: 		100 a.a.
99 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chain A: E.C.6.3.5.7  - glutaminyl-tRNA synthase (glutamine-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O = L-glutaminyl-tRNA(Gln) + L-glutamate + ADP + phosphate + H+
L-glutamyl-tRNA(Gln)
 + L-glutamine
 + ATP
 + H2O
 = L-glutaminyl-tRNA(Gln)
 + L-glutamate
 + ADP
 + phosphate
 + H(+)
   Enzyme class 3: Chains B, C: E.C.6.3.5.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
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: 10.1126/science.1127156 Science 312:1954-1958 (2006)
PubMed id: 16809541  
 
 
Ammonia channel couples glutaminase with transamidase reactions in GatCAB.
A.Nakamura, M.Yao, S.Chimnaronk, N.Sakai, I.Tanaka.
 
  ABSTRACT  
 
The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylated Glu-tRNA(Gln). Here, we describe a series of crystal structures of intact GatCAB from Staphylococcus aureus in the apo form and in the complexes with glutamine, asparagine, Mn2+, and adenosine triphosphate analog. Two identified catalytic centers for the glutaminase and transamidase reactions are markedly distant but connected by a hydrophilic ammonia channel 30 A in length. Further, we show that the first U-A base pair in the acceptor stem and the D loop of tRNA(Gln) serve as identity elements essential for discrimination by GatCAB and propose a complete model for the overall concerted reactions to synthesize Gln-tRNA(Gln).
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Bacterial GatCAB complex fastens a molecular belt. (A) Front-view ribbon diagram of the overall structure of S. aureus GatCAB/glutamine complex at 2.3 Å resolution, depicted in three different colors for each subunit: blue, green, and magenta for GatA, GatB, and GatC, respectively. Glutamine in the active site of GatA is drawn as yellow stick representations, whereas the purple sphere is the magnesium ion found in the active site of GatB. ADP from the cocrystal structure with ADP-AlF[4]^- is shown together as pink sticks. This color code is used throughout all the figures. (B) Top view of annularly shaped GatC. (C) Amphipathic helices at the N terminus of GatC form a helical bundle with the hydrophobic core of GatA (hydrophobic residues are colored gray). (D) Detailed interactions between the internal loop region of GatC and GatAB complex. Conserved residues involved are labeled, with hydrogen bonds indicated ( 3.2 Å, dashed black line). Polar interactions are prominent on the C-terminal side, whereas the hydrophobic interactions are clustered on the opposite side. (E) The C terminus of GatC tightens GatAB complex, constructing an antiparallel ß sheet and a hydrophobic platform. 		Figure 2.
Fig. 2. A 30 Å long ammonia channel connects the two remote active centers of GatCAB. (A) The active site of a glutaminase reaction in GatA is composed of the conserved Ser-cis-Ser-Lys catalytic scissors shown as magenta stick representations. Residues involved in the hydrogen-bonded network (dashed black lines) in the active site are labeled. A plausible hydrolytic water molecule is colored light blue and is on the opposite side of a supposed ammonia product (orange sphere). The Fo-Fc electron density map (contoured at 3 , green mesh) calculated without the glutamine and Ser178 clearly demonstrates the tetrahedral covalent intermediate of the glutamine with Ser178. (B) The environment of the ADP binding site shown together with the omit Fo-Fc electron density map (2 , blue). Residues contributing to ADP (ball-and-stick) recognition are represented as stick models with labels. Two water molecules (light blue spheres) are coordinated to a magnesium ion (purple) and to ß phosphate. (C) The putative ammonia channel was calculated using the program CAVER (26), with the structure of the water-omitted GatCAB/glutamine complex. Glu125B blocking the ammonia transport route is shown in a space-filling representation for clarity. The channel was filled with a row of solvent molecules (light blue spheres), which interact with the conserved polar residues (colored sticks) along the pathway. A bound glutamine in GatA is drawn as spheres indicating the start point of the channel. (D) Schematic representation of the ammonia channel. Residues defining the channel are colored corresponding to their properties: red, negative; blue, positive; black, nonpolar side chain; gray, main chain. Hydrolyzed ammonia is colored orange. Strictly conserved residues are underlined and hydrogen-bonding distances are indicated (Å). The presumed movement of the Glu125B gate to open the ammonia channel is indicated by a black arrow.
 
  The above figures are reprinted by permission from the AAAs: Science (2006, 312, 1954-1958) 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
19889645 K.Yasuhira, N.Shibata, G.Mongami, Y.Uedo, Y.Atsumi, Y.Kawashima, A.Hibino, Y.Tanaka, Y.H.Lee, D.Kato, M.Takeo, Y.Higuchi, and S.Negoro (2010).
X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation.
  J Biol Chem, 285, 1239-1248.
PDB codes: 3a2p 3a2q
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.  
20606262 T.Ito, N.Kiyasu, R.Matsunaga, S.Takahashi, and S.Yokoyama (2010).
Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 66, 813-820.
PDB code: 3afh
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
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.  
19270703 N.LaRonde-LeBlanc, M.Resto, and B.Gerratana (2009).
Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.
  Nat Struct Mol Biol, 16, 421-429.
PDB code: 3dla
19074156 P.F.Wang, A.Yep, G.L.Kenyon, and M.J.McLeish (2009).
Using directed evolution to probe the substrate specificity of mandelamide hydrolase.
  Protein Eng Des Sel, 22, 103-110.  
19435325 S.Chimnaronk, F.Forouhar, J.Sakai, M.Yao, C.M.Tron, M.Atta, M.Fontecave, J.F.Hunt, and I.Tanaka (2009).
Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon.
  Biochemistry, 48, 5057-5065.
PDB codes: 2zm5 2zxu
19322199 S.Chimnaronk, T.Suzuki, T.Manita, Y.Ikeuchi, M.Yao, T.Suzuki, and I.Tanaka (2009).
RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon.
  EMBO J, 28, 1362-1373.
PDB code: 2zpa
19770506 S.Panjikar, V.Parthasarathy, V.S.Lamzin, M.S.Weiss, and P.A.Tucker (2009).
On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination.
  Acta Crystallogr D Biol Crystallogr, 65, 1089-1097.  
19085025 W.W.Han, Y.Wang, Y.H.Zhou, Y.Yao, Z.S.Li, and Y.Feng (2009).
Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches.
  J Mol Model, 15, 481-487.  
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
19509301 Y.Tanaka, S.Yamagata, Y.Kitago, Y.Yamada, S.Chimnaronk, M.Yao, and I.Tanaka (2009).
Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand.
  RNA, 15, 1498-1506.
PDB code: 2zy6
18441100 C.Pujol, M.Bailly, D.Kern, L.Maréchal-Drouard, H.Becker, and A.M.Duchêne (2008).
Dual-targeted tRNA-dependent amidotransferase ensures both mitochondrial and chloroplastic Gln-tRNAGln synthesis in plants.
  Proc Natl Acad Sci U S A, 105, 6481-6485.  
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.  
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.  
18421771 M.A.Vanoni, and B.Curti (2008).
Structure-function studies of glutamate synthases: a class of self-regulated iron-sulfur flavoenzymes essential for nitrogen assimilation.
  IUBMB Life, 60, 287-300.  
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.  
17074748 M.Bailly, S.Giannouli, M.Blaise, C.Stathopoulos, D.Kern, and H.D.Becker (2006).
A single tRNA base pair mediates bacterial tRNA-dependent biosynthesis of asparagine.
  Nucleic Acids Res, 34, 6083-6094.  
17110438 M.J.Hohn, H.S.Park, P.O'Donoghue, M.Schnitzbauer, and D.Söll (2006).
Emergence of the universal genetic code imprinted in an RNA record.
  Proc Natl Acad Sci U S A, 103, 18095-18100.  
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