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Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP

Source organism: Methanosarcina barkeri str. Fusaro
Biochemical function: metal ion binding
Biological process: selenocysteine biosynthetic process
Cellular component: cytoplasm

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EC 6.1.1.11: Serine--tRNA ligase

Reaction catalysed:
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec)
Systematic name:
L-serine:tRNA(Ser) ligase (AMP-forming)
Alternative Name(s):
  • SerRS
  • Serine translase
  • Seryl-tRNA synthetase
  • Seryl-transfer RNA synthetase
  • Seryl-transfer ribonucleate synthetase
  • Seryl-transfer ribonucleic acid synthetase

GO terms

Sequence family

Pfam Protein family (Pfam)
PF18490
Domain description: tRNA-binding domain
Occurring in:
  1. Type-2 serine--tRNA ligase
The deposited structure of PDB entry 2cja contains 2 copies of Pfam domain PF18490 (tRNA-binding domain) in Type-2 serine--tRNA ligase. Showing 1 copy in chain B.

InterPro InterPro annotations
IPR045864
Domain description: Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Occurring in:
  1. Type-2 serine--tRNA ligase
IPR006195
Domain description: Aminoacyl-tRNA synthetase, class II
Occurring in:
  1. Type-2 serine--tRNA ligase
IPR041293
Domain description: Serine-tRNA ligase type 2, tRNA-binding domain
Occurring in:
  1. Type-2 serine--tRNA ligase
IPR004503
Domain description: Serine-tRNA ligase type 2, archaea
Occurring in:
  1. Type-2 serine--tRNA ligase

Structure domains

CATH CATH domains
3.30.930.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: BirA Bifunctional Protein; domain 2
Homology: Bira Bifunctional Protein; Domain 2
Occurring in:
  1. Type-2 serine--tRNA ligase
The deposited structure of PDB entry 2cja contains 2 copies of CATH domain 3.30.930.10 (BirA Bifunctional Protein; domain 2) in Type-2 serine--tRNA ligase. Showing 1 copy in chain B.
3.30.70.1920
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Alpha-Beta Plaits
Occurring in:
  1. Type-2 serine--tRNA ligase
The deposited structure of PDB entry 2cja contains 2 copies of CATH domain 3.30.70.1920 (Alpha-Beta Plaits) in Type-2 serine--tRNA ligase. Showing 1 copy in chain B.

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