PDBsum entry 2pme

Ligase

PDB id: 2pme

Contents

Protein chain

521 a.a. *

Waters ×122

* Residue conservation analysis

PDB id:

2pme

Name:

Ligase

Title:

The apo crystal structure of the glycyl-tRNA synthetase

Structure:

Glycyl-tRNA synthetase. Chain: a. Synonym: glycine--tRNA ligase, glyrs. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: gars. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.90Å R-factor: 0.232 R-free: 0.271

Authors:

W.Xie

Key ref:

W.Xie et al. (2007). Long-range structural effects of a Charcot-Marie-Tooth disease-causing mutation in human glycyl-tRNA synthetase. Proc Natl Acad Sci U S A, 104, 9976-9981. PubMed id: 17545306 DOI: 10.1073/pnas.0703908104

Date:

21-Apr-07 Release date: 22-May-07

Protein chain

P41250  (GARS_HUMAN) -  Glycine--tRNA ligase from Homo sapiens

Seq: 739 a.a.

Struc: 521 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.- - ?????
• Enzyme class 3: E.C.6.1.1.14 - glycine--tRNA ligase.
• Reaction: tRNA(Gly) + glycine + ATP = glycyl-tRNA(Gly) + 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

DOI no: 10.1073/pnas.0703908104

Proc Natl Acad Sci U S A 104:9976-9981 (2007)

PubMed id: 17545306

Long-range structural effects of a Charcot-Marie-Tooth disease-causing mutation in human glycyl-tRNA synthetase.

W.Xie, L.A.Nangle, W.Zhang, P.Schimmel, X.L.Yang.

ABSTRACT

Functional expansion of specific tRNA synthetases in higher organisms is well documented. These additional functions may explain why dominant mutations in glycyl-tRNA synthetase (GlyRS) and tyrosyl-tRNA synthetase cause Charcot-Marie-Tooth (CMT) disease, the most common heritable disease of the peripheral nervous system. At least 10 disease-causing mutant alleles of GlyRS have been annotated. These mutations scatter broadly across the primary sequence and have no apparent unifying connection. Here we report the structure of wild type and a CMT-causing mutant (G526R) of homodimeric human GlyRS. The mutation is at the site for synthesis of glycyl-adenylate, but the rest of the two structures are closely similar. Significantly, the mutant form diffracts to a higher resolution and has a greater dimer interface. The extra dimer interactions are located approximately 30 A away from the G526R mutation. Direct experiments confirm the tighter dimer interaction of the G526R protein. The results suggest the possible importance of subtle, long-range structural effects of CMT-causing mutations at the dimer interface. From analysis of a third crystal, an appended motif, found in higher eukaryote GlyRSs, seems not to have a role in these long-range effects.

Selected figure(s)

Figure 4.
Fig. 4. G526R mutation strengthens dimer interaction. (A) "Back" view of the GlyRS subunit that shows the dimerization interface. This view is related to the "front" view in Fig. 1A by a 180° rotation along the y axis. The three patches that give dimer interactions are colored: patch 1 (F78–T137) in cyan, patch 2 (F224–L242) in green, and patch 3 (L252–E291) in gold. (B) Loose dimerization interface of wild-type GlyRS generated by mapping the surface area of one subunit that is within 7 Å of the other. (C) The same dimerization interface generated for G526R mutant. The extra dimer interface, absent in the wild-type enzyme, lies in the anticodon recognition domain and is 30 Å away from the mutation site. (D) Analytical ultracentrifugation experiment showing that more dimers are formed by G526R mutant than by wild-type GlyRS. (Inset) Immunoprecipitation experiment showing that G526R mutant GlyRS pulled down more endogenous GlyRS than did the wild-type GlyRS, presumably by forming dimers.

Figure 5.
Fig. 5. G41R mutation in TyrRS resembles G526R mutation in GlyRS. (A) Active site of human TyrRS bound with substrate analog tyrosinol. (B) CMT-causing mutation G41R would block tyrosine binding in a similar way as G526R in GlyRS blocks binding of the AMP moiety.

Figures were selected by an automated process.