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PDBsum entry 3adb
Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Transferase/RNA PDB id
3adb

 

 

 

 

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Contents
Protein chains
250 a.a. *
DNA/RNA
Ligands
PO4
ANP
Metals
_MG
Waters ×159
* Residue conservation analysis
PDB id:
3adb
Name: Transferase/RNA
Title: Crystal structure of o-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and amppnp (crystal type 1)
Structure: L-seryl-tRNA(sec) kinase. Chain: a, b. Synonym: o-phosphoseryl-tRNA(sec) kinase, pstk. Engineered: yes. Selenocysteine tRNA. Chain: c, d. Engineered: yes
Source: Methanocaldococcus jannaschii. Methanococcus jannaschii. Organism_taxid: 243232. Strain: dsm 2661. Gene: mj1538. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Methanopyrus kandleri.
Resolution:
2.80Å     R-factor:   0.228     R-free:   0.269
Authors: Y.Itoh,S.Chiba,S.Sekine,S.Yokoyama
Key ref: S.Chiba et al. (2010). Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine. Mol Cell, 39, 410-420. PubMed id: 20705242
Date:
18-Jan-10     Release date:   28-Jul-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q58933  (PSTK_METJA) -  L-seryl-tRNA(Sec) kinase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Seq:
Struc: 		248 a.a.
250 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  G-G-C-C-G-C-C-G-C-C-A-C-C-G-G-G-G-U-G-G-U-C-C-C-C-G-G-G-C-C-G-G-A-C-U-U-C-A-G- 92 bases
  G-G-C-C-G-C-C-G-C-C-A-C-C-G-G-G-G-U-G-G-U-C-C-C-C-G-G-G-C-C-G-G-A-C-U-U-C-A-G- 92 bases

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.164  - O-phosphoseryl-tRNA(Sec) kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-seryl-tRNA(Sec) + ATP = O-phospho-L-seryl-tRNA(Sec) + ADP
L-seryl-tRNA(Sec)
 + ATP
 = O-phospho-L-seryl-tRNA(Sec)
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity 		+ ADP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Mol Cell 39:410-420 (2010)
PubMed id: 20705242  
 
 
Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.
S.Chiba, Y.Itoh, S.Sekine, S.Yokoyama.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20870747 R.L.Sherrer, Y.Araiso, C.Aldag, R.Ishitani, J.M.Ho, D.Söll, and O.Nureki (2011).
C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec).
  Nucleic Acids Res, 39, 1034-1041.
PDB code: 3am1
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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