Motion in Seryl-tRNA synthetase [strnasyn]

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Classification Known Fragment Motion, Hinge Mechanism [F-h-2]

Structures
1SER Conformation 1 [ PartsList ]
1SES Conformation 2 [ PartsList ]
1SET Conformation 3 [ PartsList ]

Description
Two connected helices project out from protein like stalk. Upon binding tRNA these helices bend and rotate 20 degrees with respect to rest of protein.
In the structures of Thermus Thermophilus Aspartyl tRNA synthetase alone and bound to its substrate aspartyl adenylate, there is an 8 degree rotation between these structures and the structure of a different amino-acyl tRNA synthetase from yeast solved by Ruff et al. This is almost definitely a hinge-type motion.
This a type II tRNA synthetase. It is of the same class as the Ser-tRNA synethase, which was solved by Cusack (Biou et al.). This structure has long antennae for recognizing the tRNA, that adopts a different form in two different crystal forms.

Particular values describing motion
Creation Date = 19970822
Experimental Methods = x (Traditional x-ray)
Maximum Rotation (degrees) = 20
Modification Date = 1998-06-29 12:42:44.000

References
H Belrhali, A Yaremchuk, M Tukalo, K Larsen, C Berthet-Colominas, R Leberman, B Beijer, B Sproat, J Als-Nielsen, G Grubel and a et (1994). Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Science. 263: 1432-1436. [Medline info for 94174279]
V Biou, A Yaremchuk, M Tukalo and S Cusack (1994). The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science. 263: 1404-1410. [Medline info for 94174274]

GO terms associated with structures
Molecular functiontRNA ligase activity, serine-tRNA ligase activity, ATP binding
Biological processtRNA aminoacylation for protein translation, seryl-tRNA aminoacylation

Morphs

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Best representative
Morph Morph name Structure #1 Structure #2 Residues
Seryl tRNA synthetase 1ser [ ] 1ses [ ] 421


Automatic morphs
Morph Morph name Structure #1 Structure #2 Residues
va1serB-1sryA Seryl-tRNA Synthetase (E.C. 6. 1ser [ B ] 1sry [ A ] 421
va1serB-1sesA Seryl-tRNA Synthetase (E.C. 6. 1ser [ B ] 1ses [ A ] 421
va1serB-1setA Seryl-tRNA Synthetase (E.C. 6. 1ser [ B ] 1set [ A ] 421
va1setB-1serB Seryl-tRNA Synthetase (E.C. 6. 1set [ B ] 1ser [ B ] 421
va1sesB-1sryA Seryl-tRNA Synthetase (E.C. 6. 1ses [ B ] 1sry [ A ] 421
va1sesB-1setA Seryl-tRNA Synthetase (E.C. 6. 1ses [ B ] 1set [ A ] 421
va1sryB-1setA Seryl-tRNA Synthetase (E.C. 6. 1sry [ B ] 1set [ A ] 421
va1sryB-1serB Seryl-tRNA Synthetase (E.C. 6. 1sry [ B ] 1ser [ B ] 421
va1sesB-1serB Seryl-tRNA Synthetase (E.C. 6. 1ses [ B ] 1ser [ B ] 421
va1setB-1sryA Seryl-tRNA Synthetase (E.C. 6. 1set [ B ] 1sry [ A ] 421
va1sryB-1sesA Seryl-tRNA Synthetase (E.C. 6. 1sry [ B ] 1ses [ A ] 421
va1setB-1sesA Seryl-tRNA Synthetase (E.C. 6. 1set [ B ] 1ses [ A ] 421

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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_ yale.edu