PDBsum entry 5f7t

Ligase

PDB id

5f7t

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Contents

			Protein chains

					134 a.a.

			Metals

					_ZN ×8

			Waters ×52

PDB id:

5f7t

Links

Name:

Ligase

Title:

Trim5 b-box2 and coiled-coil chimera

Structure:

Tripartite motif-containing protein 5,serine--tRNA ligase, tripartite motif-containing protein 5. Chain: e, f, h, l. Synonym: trim5alpha,seryl-tRNA synthetase,serrs. Engineered: yes

Source:

Macaca mulatta, thermus thermophilus (strain hb27 / atcc baa-163 / dsm 7039). Rhesus macaque. Organism_taxid: 9544, 262724. Strain: hb27 / atcc baa-163 / dsm 7039. Gene: trim5, sers, tt_c0520. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.29Å

R-factor:

0.225

R-free:

0.256

Authors:

J.M.Wagner,G.Doss,O.Pornillos

Key ref:

J.M.Wagner et al. (2016). Mechanism of b-Box 2 domain-Mediated higher-Order ass of the retroviral restriction factor trim5 alpha.. Elife, 5, . PubMed id: 27253059

Date:

08-Dec-15

Release date:

15-Jun-16

PROCHECK

	Headers

	References

Protein chains

P34945 (SYS_THET2) - Serine--tRNA ligase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: Struc:					421 a.a. 134 a.a.*

Protein chains

Q0PF16 (TRIM5_MACMU) - Tripartite motif-containing protein 5 from Macaca mulatta

Seq: Struc:					497 a.a. 134 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 92 residue positions (black crosses)



		Enzyme reactions

Enzyme class 1:

E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

Enzyme class 2:

E.C.6.1.1.11 - serine--tRNA ligase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

1.	tRNA(Ser) + L-serine + ATP = L-seryl-tRNA(Ser) + AMP + diphosphate + H⁺
2.	tRNA(Sec) + L-serine + ATP = L-seryl-tRNA(Sec) + AMP + diphosphate + H⁺

tRNA(Ser)	+	L-serine	+	ATP	=	L-seryl-tRNA(Ser)	+	AMP	+	diphosphate	+	H(+)

tRNA(Sec)	+	L-serine	+	ATP	=	L-seryl-tRNA(Sec)	+	AMP	+	diphosphate	+	H(+)

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