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PDBsum entry 2e7i
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protein ligands Protein-protein interface(s) links
Lyase PDB id
2e7i

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
344 a.a. *
Ligands
SO4 ×5
PLP
Waters ×72
* Residue conservation analysis
PDB id:
2e7i
Name: Lyase
Title: Crystal structure of sep-trna:cys-tRNA synthase from archaeoglobus fulgidus
Structure: Sep-trna:cys-tRNA synthase. Chain: a, b. Synonym: hypothetical protein af_0028. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.00Å     R-factor:   0.271     R-free:   0.318
Authors: R.Fukunaga,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Fukunaga and S.Yokoyama (2007). Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus. J Mol Biol, 370, 128-141. PubMed id: 17512006 DOI: 10.1016/j.jmb.2007.04.050
Date:
10-Jan-07     Release date:   17-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O30207  (SPSS1_ARCFU) -  O-phospho-L-seryl-tRNA:Cys-tRNA synthase 1 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		371 a.a.
344 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.5.1.73  - O-phospho-L-seryl-tRNA:Cys-tRNA synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: O-phospho-L-seryl-tRNA(Cys) + hydrogen sulfide + H+ = L-cysteinyl- tRNA(Cys) + phosphate
O-phospho-L-seryl-tRNA(Cys)
 + hydrogen sulfide
 + H(+)
 = L-cysteinyl- tRNA(Cys)
 + phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/j.jmb.2007.04.050 J Mol Biol 370:128-141 (2007)
PubMed id: 17512006  
 
 
Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus.
R.Fukunaga, S.Yokoyama.
 
  ABSTRACT  
 
In the ancient organisms, methanogenic archaea, lacking the canonical cysteinyl-tRNA synthetase, Cys-tRNA(Cys) is produced by an indirect pathway, in which O-phosphoseryl-tRNA synthetase ligates O-phosphoserine (Sep) to tRNA(Cys) and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys). In this study, the crystal structure of SepCysS from Archaeoglobus fulgidus has been determined at 2.4 A resolution. SepCysS forms a dimer, composed of monomers bearing large and small domains. The large domain harbors the seven-stranded beta-sheet, which is typical of the pyridoxal 5'-phosphate (PLP)-dependent enzymes. In the active site, which is located near the dimer interface, PLP is covalently bound to the side-chain of the conserved Lys209. In the proximity of PLP, a sulfate ion is bound by the side-chains of the conserved Arg79, His103, and Tyr104 residues. The active site is located deep within the large, basic cleft to accommodate Sep-tRNA(Cys). On the basis of the surface electrostatic potential, the amino acid residue conservation mapping, the position of the bound sulfate ion, and the substrate amino acid binding manner in other PLP-dependent enzymes, a binding model of Sep-tRNA(Cys) to SepCysS was constructed. One of the three strictly conserved Cys residues (Cys39, Cys42, or Cys247), of one subunit may play a crucial role in the catalysis in the active site of the other subunit.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The internal aldimine Lys209-PLP and the sulfate ion in the active site. (a) Architecture of the active site (stereo view). The main-chain traces of subunits A and B are shown by light blue and light green tubes, respectively. The internal aldimine Lys209-PLP (cyan) and the sulfate ion are shown by ball and stick models. Hydrogen bonds are shown as pink broken lines. (b) The |F[o]–F[c]| simulated-annealing omit electron density maps (3.0σ) for Lys209-PLP and the sulfate ion are shown in blue and green, respectively. (c) The |F[o]–F[c]| simulated-annealing omit electron density maps (3.0σ) for Lys209 and the sulfate ion are shown in blue and green, respectively, in the active site of molecule B of the SeMet SepCysS structure.
Figure 8.
Figure 8. Active site comparison between SepCysS and CsdB and the Sep-Ado76 binding model. (a) Architecture of the SepCysS active site (stereo view). The main-chain traces are colored as in Figure 7(a). The internal aldimine Lys209-PLP (cyan) and the sulfate ion are shown by ball and stick models. (b) Architecture of the CsdB active site (PDB ID, 1KMK) (stereo view). The main-chain traces are colored as in Figure 7(b). The internal aldimine Lys226-PLP and the selenocysteine are shown by cyan and pink ball and stick models, respectively. The Cys364 side-chain is perselenided. The coordinates of one of the oxygen atoms in the α-COO^− group of the selenocysteine is missing in PDB ID, 1KMK. (c) Sep-Ado76 binding model. Sep-Ado76 is shown by a pink ball and stick model. (d) Sep-Ado76 binding model on the conservation mapping shown in Figure 6.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 128-141) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18798524 D.Su, M.J.Hohn, S.Palioura, R.L.Sherrer, J.Yuan, D.Söll, and P.O'Donoghue (2009).
How an obscure archaeal gene inspired the discovery of selenocysteine biosynthesis in humans.
  IUBMB Life, 61, 35-39.  
19608919 S.Palioura, R.L.Sherrer, T.A.Steitz, D.Söll, and M.Simonovic (2009).
The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation.
  Science, 325, 321-325.
PDB code: 3hl2
20042123 T.K.Bhatt, C.Kapil, S.Khan, M.A.Jairajpuri, V.Sharma, D.Santoni, F.Silvestrini, E.Pizzi, and A.Sharma (2009).
A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum.
  BMC Genomics, 10, 644.  
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.  
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.  
18093968 O.M.Ganichkin, X.M.Xu, B.A.Carlson, H.Mix, D.L.Hatfield, V.N.Gladyshev, and M.C.Wahl (2008).
Structure and catalytic mechanism of eukaryotic selenocysteine synthase.
  J Biol Chem, 283, 5849-5865.
PDB codes: 3bc8 3bca 3bcb
18559341 S.I.Hauenstein, and J.J.Perona (2008).
Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei.
  J Biol Chem, 283, 22007-22017.  
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
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.

 

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