spacer
spacer

PDBsum entry 3l4g

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Ligase PDB id
3l4g
Jmol PyMol
Contents
Protein chains
(+ 0 more) 318 a.a. *
(+ 2 more) 589 a.a. *
508 a.a. *
349 a.a. *
Ligands
PHE ×8
* Residue conservation analysis
PDB id:
3l4g
Name: Ligase
Title: Crystal structure of homo sapiens cytoplasmic phenylalanyl-t synthetase
Structure: Phenylalanyl-tRNA synthetase alpha chain. Chain: a, c, e, g, i, k, m, o. Synonym: cytoplasmic phenylalanyl-tRNA synthetase alpha sub phenylalanine--tRNA ligase alpha chain, phers, cml33. Engineered: yes. Phenylalanyl-tRNA synthetase beta chain. Chain: b, d, f, h, j, l, n, p. Synonym: cytoplasmic phenylalanyl-tRNA synthetase beta subu phenylalanine--tRNA ligase beta chain, phers.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: farsa, fars, farsl, farsla. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: farsb, farslb, frsb, hspc173.
Resolution:
3.30Å     R-factor:   0.242     R-free:   0.287
Authors: I.Finarov,N.Moor,N.Kessler,L.Klipcan,M.G.Safro
Key ref: I.Finarov et al. (2010). Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns. Structure, 18, 343-353. PubMed id: 20223217
Date:
20-Dec-09     Release date:   09-Mar-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9Y285  (SYFA_HUMAN) -  Phenylalanine--tRNA ligase alpha subunit
Seq:
Struc:
508 a.a.
318 a.a.
Protein chains
Pfam   ArchSchema ?
Q9NSD9  (SYFB_HUMAN) -  Phenylalanine--tRNA ligase beta subunit
Seq:
Struc:
 
Seq:
Struc:
589 a.a.
589 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9Y285  (SYFA_HUMAN) -  Phenylalanine--tRNA ligase alpha subunit
Seq:
Struc:
508 a.a.
508 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Y285  (SYFA_HUMAN) -  Phenylalanine--tRNA ligase alpha subunit
Seq:
Struc:
508 a.a.
349 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 21 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: 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
Bound ligand (Het Group name = PHE)
corresponds exactly
+ tRNA(Phe)
= AMP
+ 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     membrane   4 terms 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
Structure 18:343-353 (2010)
PubMed id: 20223217  
 
 
Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.
I.Finarov, N.Moor, N.Kessler, L.Klipcan, M.G.Safro.
 
  ABSTRACT  
 
The existence of three types of phenylalanyl-tRNA synthetase (PheRS), bacterial (alphabeta)(2), eukaryotic/archaeal cytosolic (alphabeta)(2), and mitochondrial alpha, is a prominent example of structural diversity within the aaRS family. PheRSs have considerably diverged in primary sequences, domain compositions, and subunit organizations. Loss of the anticodon-binding domain B8 in human cytosolic PheRS (hcPheRS) is indicative of variations in the tRNA(Phe) binding and recognition as compared to bacterial PheRSs. We report herein the crystal structure of hcPheRS in complex with phenylalanine at 3.3 A resolution. A novel structural module has been revealed at the N terminus of the alpha subunit. It stretches out into the solvent of approximately 80 A and is made up of three structural domains (DBDs) possessing DNA-binding fold. The dramatic reduction of aminoacylation activity for truncated N terminus variants coupled with structural data and tRNA-docking model testify that DBDs play crucial role in hcPheRS activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082706 I.Mermershtain, I.Finarov, L.Klipcan, N.Kessler, H.Rozenberg, and M.G.Safro (2011).
Idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP.
  Protein Sci, 20, 160-167.
PDB code: 3pco
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