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PDBsum entry 1b7y

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1b7y
Jmol
Contents
Protein chains
265 a.a. *
775 a.a. *
Ligands
FYA
Metals
_MG
Waters ×239
* Residue conservation analysis
PDB id:
1b7y
Name: Ligase
Title: Phenylalanyl tRNA synthetase complexed with phenylalaninyl-a
Structure: Protein (phenylalanyl-tRNA synthetase). Chain: a. Synonym: phers. Protein (phenylalanyl-tRNA synthetase). Chain: b. Synonym: phers. Ec: 6.1.1.20
Source: Thermus thermophilus. Organism_taxid: 274. Cellular_location: cytoplasm. Cellular_location: cytoplasm
Biol. unit: Tetramer (from PDB file)
Resolution:
2.50Å     R-factor:   0.230     R-free:   0.267
Authors: L.Reshetnikova,N.Moor,O.Lavrik,D.G.Vassylyev
Key ref:
L.Reshetnikova et al. (1999). Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue. J Mol Biol, 287, 555-568. PubMed id: 10092459 DOI: 10.1006/jmbi.1999.2617
Date:
26-Jan-99     Release date:   26-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P27001  (SYFA_THETH) -  Phenylalanine--tRNA ligase alpha subunit
Seq:
Struc:
350 a.a.
265 a.a.
Protein chain
Pfam   ArchSchema ?
P27002  (SYFB_THETH) -  Phenylalanine--tRNA ligase beta subunit
Seq:
Struc:
 
Seq:
Struc:
785 a.a.
775 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.6.1.1.20  - Phenylalanine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl- tRNA(Phe)
ATP
+ L-phenylalanine
+ tRNA(Phe)
=
AMP
Bound ligand (Het Group name = FYA)
matches with 69.70% similarity
+ diphosphate
+ L-phenylalanyl- tRNA(Phe)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.2617 J Mol Biol 287:555-568 (1999)
PubMed id: 10092459  
 
 
Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.
L.Reshetnikova, N.Moor, O.Lavrik, D.G.Vassylyev.
 
  ABSTRACT  
 
The crystal structures of Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) complexed with phenylalanine and phenylalaninyl-adenylate (PheOH-AMP), the synthetic analogue of phenylalanyl-adenylate, have been determined at 2.7A and 2.5A resolution, respectively. Both Phe and PheOH-AMP are engulfed in the active site cleft of the catalytic alpha-subunit of PheRS, and neither makes contact with the PheRS beta-subunit. The conformations and binding of Phe are almost identical in both complexes. The recognition of Phe by PheRS is achieved through a mixture of multiple van der Waals interactions and hydrogen bonds. The side-chain of the Phe substrate is sandwiched between the hydrophobic side-chains of Phealpha258 and Phealpha260 on one side, and the main-chain atoms of the two adjacent beta-strands on the other. The side-chains of Valalpha261 and Alaalpha314 form the back wall of the amino acid binding pocket. In addition, PheRS residues (Trpalpha149, Seralpha180, Hisalpha178, Argalpha204, Glnalpha218, and Glualpha220) form a total of seven hydrogen bonds with the main-chain atoms of Phe. The conformation of PheOH-AMP and the network of interactions of its AMP moiety with PheRS are reminiscent of the other class II synthetases. The structural similarity between PheRS and histidyl-tRNA synthetase extends to the amino acid binding site, which is normally unique for each enzyme. The complex structures suggest that the PheRS beta-subunit may affect the first step of the reaction (formation of phenylalanyl-adenylate) through the metal-mediated conserved alpha/beta-subunit interface. The modeling of tyrosine in the active site of PheRS revealed no apparent close contacts between tyrosine and the PheRS residues. This result implies that the proofreading mechanism against activated tyrosine, rather than direct recognition, may play the major role in the PheRS specificity.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo views of the active sites in the PheRS/Phe and PheRS/PheOH-AMP complexes. Only residues from the PheRS α-subunit are shown. The proteins and the substrates are shown as a ball-and-stick models. The bonds between the atoms are shown as yellow and green sticks for the protein residues and the substrates, respectively. The atoms are shown as small spheres with atom-dependent colors. The Figure was produced using the MOLSCRIPT program (Kraulis, 1991). (a) The amino acid binding site in the PheRS/Phe complex. (b) The AMP binding site in the PheRS/PheOH-AMP complex.
Figure 5.
Figure 5. Schematic drawing of the interactions between PheRS and PheOH-AMP in the PheRS/PheOH-AMP complex structure. The protein/substrate contacts are shown as arrows. The hydrophobic residues and interactions are colored in green, whereas the polar residues and the hydrogen bonds are shown in red. MC, main chain.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 555-568) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
18568158 J.S.Cisar, and D.S.Tan (2008).
Small molecule inhibition of microbial natural product biosynthesis-an emerging antibiotic strategy.
  Chem Soc Rev, 37, 1320-1329.  
  17768348 I.Levin, N.Kessler, N.Moor, L.Klipcan, E.Koc, P.Templeton, L.Spremulli, and M.Safro (2007).
Purification, crystallization and preliminary X-ray characterization of a human mitochondrial phenylalanyl-tRNA synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 761-764.  
17185419 J.Ling, H.Roy, and M.Ibba (2007).
Mechanism of tRNA-dependent editing in translational quality control.
  Proc Natl Acad Sci U S A, 104, 72-77.  
17003130 H.M.Sasaki, S.Sekine, T.Sengoku, R.Fukunaga, M.Hattori, Y.Utsunomiya, C.Kuroishi, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2006).
Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 103, 14744-14749.
PDB code: 2cxi
15657145 M.A.Swairjo, and P.R.Schimmel (2005).
Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase.
  Proc Natl Acad Sci U S A, 102, 988-993.
PDB codes: 1yfr 1yfs 1yft 1ygb
15562516 N.Rekha, S.M.Machado, C.Narayanan, A.Krupa, and N.Srinivasan (2005).
Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways.
  Proteins, 58, 339-353.  
16338408 O.Kotik-Kogan, N.Moor, D.Tworowski, and M.Safro (2005).
Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase.
  Structure, 13, 1799-1807.
PDB codes: 2akw 2aly 2amc
14742205 D.Beyer, H.P.Kroll, R.Endermann, G.Schiffer, S.Siegel, M.Bauser, J.Pohlmann, M.Brands, K.Ziegelbauer, D.Haebich, C.Eymann, and H.Brötz-Oesterhelt (2004).
New class of bacterial phenylalanyl-tRNA synthetase inhibitors with high potency and broad-spectrum activity.
  Antimicrob Agents Chemother, 48, 525-532.  
12591875 S.W.Jordan, and J.E.Cronan (2003).
The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase.
  J Bacteriol, 185, 1582-1589.  
12382236 I.A.Vasil'eva, V.N.Ankilova, O.I.Lavrik, and N.A.Moor (2002).
tRNA discrimination by T. thermophilus phenylalanyl-tRNA synthetase at the binding step.
  J Mol Recognit, 15, 188-196.  
11679717 R.Fishman, V.Ankilova, N.Moor, and M.Safro (2001).
Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.
  Acta Crystallogr D Biol Crystallogr, 57, 1534-1544.
PDB code: 1jjc
10969988 A.K.Forrest, R.L.Jarvest, L.M.Mensah, P.J.O'Hanlon, A.J.Pope, and R.J.Sheppard (2000).
Aminoalkyl adenylate and aminoacyl sulfamate intermediate analogues differing greatly in affinity for their cognate Staphylococcus aureus aminoacyl tRNA synthetases.
  Bioorg Med Chem Lett, 10, 1871-1874.  
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
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.