2DXI: Glutamyl-tRNA synthetase

2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol. Determined by X-ray diffraction at 2.2 Å resolution. Released 31 Oct 2006.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Thermus thermophilus
Chains: 4
Atoms: 11,272
Mol. weight: 157.52 kDa
Ligands: GAU, ATP, MG
Released: 31 Oct 2006

Explore 2DXI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2DXI contains 65 α-helices and 44 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 31 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	14	1
β-strand	15	1	2
α-helix	16-31	16
β-strand	35-38	4	1
β-strand	40	1	3
α-helix	52-62	11
β-strand	69	1	1
β-strand	70	1	4
β-strand	74	1	4
β-strand	81	1	3
α-helix	82-84	3
α-helix	86-98	13
β-strand	102-105	4	5
α-helix	109-119	11
α-helix	125-128	4
α-helix	131-139	9
β-strand	145-148	4	5
β-strand	155-160	6	6
β-strand	164-169	6	6
α-helix	170-172	3
β-strand	177-179	3	5
α-helix	184	1
β-strand	185	1	5
α-helix	186	1
α-helix	187-197	11
β-strand	202-206	5	6
α-helix	207-212	6
α-helix	213-223	11
β-strand	229-233	5	6
α-helix	234-236	3
β-strand	237	1	7
β-strand	243	1	7
β-strand	252	1	2
α-helix	253-258	6
α-helix	263-271	9
β-strand	275	1	8
α-helix	286-292	7
α-helix	295-297	3
β-strand	298	1	8
β-strand	304	1	7
α-helix	307-316	10
α-helix	317-321	5
α-helix	324-337	14
α-helix	345-355	11
α-helix	356-358	3
α-helix	364-368	5
α-helix	370-372	3
α-helix	381-402	22
α-helix	409-422	14
α-helix	427-439	13
α-helix	447-454	8
α-helix	456-467	12

Chain B: 34 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
α-helix	14	1
β-strand	15	1	10
α-helix	16-31	16
β-strand	35-38	4	9
β-strand	40	1	11
α-helix	52-62	11
β-strand	69	1	9
β-strand	70	1	12
β-strand	74	1	12
β-strand	81	1	11
α-helix	82-84	3
α-helix	86-98	13
β-strand	102-105	4	13
α-helix	109-119	11
α-helix	125-128	4
α-helix	131-139	9
β-strand	145-148	4	13
β-strand	155-160	6	14
β-strand	164-169	6	14
α-helix	170-172	3
β-strand	177-179	3	13
α-helix	184	1
β-strand	185	1	13
α-helix	186	1
α-helix	187-197	11
β-strand	202-206	5	14
α-helix	207-212	6
α-helix	213-223	11
α-helix	225-228	4
β-strand	229-233	5	14
α-helix	234-236	3
β-strand	237	1	15
β-strand	243	1	15
β-strand	252	1	10
α-helix	253-258	6
α-helix	263-271	9
β-strand	275	1	16
α-helix	286-292	7
α-helix	295-297	3
β-strand	298	1	16
α-helix	303	1
β-strand	304	1	15
α-helix	305	1
α-helix	307-316	10
α-helix	317-321	5
α-helix	324-337	14
α-helix	345-355	11
α-helix	356-358	3
α-helix	364-368	5
α-helix	370-372	3
α-helix	381-403	23
α-helix	409-422	14
α-helix	427-439	13
α-helix	447-453	7
α-helix	456-467	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
tRNA	C, D	RNA	75
glutamyl-tRNA synthetase	A, B	protein	468	Thermus thermophilus	P27000 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>2DXI_1 tRNA (chains C, D)
GGCCCCAUCGUCUAGCGGUUAGGACGCGGCCCUCUCAAGGCCGAAACGGGGGUUCGAUUC
CCCCUGGGGUCACCA

Sequence of entity 2 (A, B), FASTA

>2DXI_2 glutamyl-tRNA synthetase (chains A, B)
MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAAL
KWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKG
GYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLK
SDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPD
KTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSL
GGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFD
TLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFA
AEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA

Ligands and cofactors

ID	Name	Formula	Copies
GAU	(4S)-4-amino-5-hydroxypentanoic acid	C5 H11 N O3	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Sekine, S., Shichiri, M., Bernier, S. et al. Structure (2006) 14:1791-1799. DOI 10.1016/j.str.2006.10.005 · PubMed

Other PDB entries of the same protein (UniProt P27000 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1J09 1.8 Å, Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP…
1N75 1.9 Å, Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP.
2CUZ 1.98 Å, Glutamyl-tRNA synthetase from Thermus thermophilus in complex with L-glutamate
1N78 2.1 Å, Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with…
1G59 2.4 Å, Glutamyl-tRNA synthetase complexed with trna(glu).
1N77 2.4 Å, Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with…
2CV0 2.4 Å, Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu) and…
2CV1 2.41 Å, Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu), ATP, and…
1GLN 2.5 Å, Architectures of class-defining and specific domains of glutamyl-tRNA synthetase
2CV2 2.69 Å, Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu) and an…

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