PDBsum entry 3al0

Ligase/RNA

PDB id: 3al0

Contents

Protein chains

472 a.a. *

482 a.a. *

564 a.a. *

DNA/RNA

Ligands

GSU

Metals

_ZN

* Residue conservation analysis

PDB id:

3al0

Name:

Ligase/RNA

Title:

Crystal structure of the glutamine transamidosome from thermotoga maritima in the glutamylation state.

Structure:

Glutamyl-tRNA(gln) amidotransferase subunit a. Chain: a. Synonym: glu-adt subunit a. Engineered: yes. Aspartyl/glutamyl-tRNA(asn/gln) amidotransferase subunit b. Chain: b. Synonym: asp/glu-adt subunit b. Engineered: yes. Glutamyl-tRNA(gln) amidotransferase subunit c,linker,

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: atcc 43589 / msb8 / dsm 3109 / jcm 10099. Gene: gata, tm_1272. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: gatb, tm_1273. Thermotoga maritima, synthetic construct. Organism_taxid: 243274, 32630.

Resolution:

3.37Å R-factor: 0.199 R-free: 0.269

Authors:

T.Ito,S.Yokoyama

Key ref:

T.Ito and S.Yokoyama (2010). Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions. Nature, 467, 612-616. PubMed id: 20882017

Date:

19-Jul-10 Release date: 29-Sep-10

Protein chain

Q9X0Z9  (GATA_THEMA) -  Glutamyl-tRNA(Gln) amidotransferase subunit A from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 475 a.a.

Struc: 472 a.a.

Protein chain

Q9X100  (GATB_THEMA) -  Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 482 a.a.

Struc: 482 a.a.

Protein chain

Q9WY94  (GATC_THEMA) -  Glutamyl-tRNA(Gln) amidotransferase subunit C from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 96 a.a.

Struc: 564 a.a.*

Protein chain

Q9X2I8  (SYE2_THEMA) -  Glutamate--tRNA ligase 2 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 487 a.a.

Struc: 564 a.a.*

* PDB and UniProt seqs differ at 16 residue positions (black crosses)

DNA/RNA chain

U-G-G-G-A-G-G-U-C-G-U-C-U-A-A-C-G-G-U-A-G-G-A-C-G-G-C-G-G-A-C-U-C-U-G-G-A-U-C- 74 bases

Enzyme reactions

• Enzyme class 2: Chain A: E.C.6.3.5.7 - glutaminyl-tRNA synthase (glutamine-hydrolyzing).
• Reaction: L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O = L-glutaminyl-tRNA(Gln) + L-glutamate + ADP + phosphate + H⁺

L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O = L-glutaminyl-tRNA(Gln) (Bound ligand (Het Group name = GSU) matches with 47.50% similarity) + L-glutamate + ADP + phosphate + H(+)

• Enzyme class 3: Chains B, C: E.C.6.3.5.- - ?????
• Enzyme class 4: Chain C: E.C.6.1.1.17 - glutamate--tRNA ligase.
• Reaction: tRNA(Glu) + L-glutamate + ATP = L-glutamyl-tRNA(Glu) + AMP + diphosphate

tRNA(Glu) + L-glutamate + ATP = L-glutamyl-tRNA(Glu) (Bound ligand (Het Group name = GSU) matches with 52.78% similarity) + AMP + diphosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Nature 467:612-616 (2010)

PubMed id: 20882017

Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.

T.Ito, S.Yokoyama.

ABSTRACT

No abstract given.