2c78
From Proteopedia
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|PDB= 2c78 |SIZE=350|CAPTION= <scene name='initialview01'>2c78</scene>, resolution 1.4Å | |PDB= 2c78 |SIZE=350|CAPTION= <scene name='initialview01'>2c78</scene>, resolution 1.4Å | ||
|SITE= <scene name='pdbsite=AC1:Pul+Binding+Site+For+Chain+A'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Pul+Binding+Site+For+Chain+A'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PUL:(1S,2S,3E,5E,7E,10S,11S,12S)-12-[(2R,4E,6E,8Z,10R,12E,14E,16Z,18S,19Z)-10,18-DIHYDROXY-12,16,19-TRIMETHYL-11,22-DIOXOOXACYCLODOCOSA-4,6,8,12,14,16,19-HEPTAEN-2-YL]-2,11-DIHYDROXY-1,10-DIMETHYL-9-OXOTRIDECA-3,5,7-TRIEN-1-YL+6-DEOXY-2,4-DI-O-METHYL-BETA-L-GALACTOPYRANOSIDE'>PUL</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/dGTPase dGTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/dGTPase dGTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c78 OCA], [http://www.ebi.ac.uk/pdbsum/2c78 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2c78 RCSB]</span> | ||
}} | }} | ||
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[[Category: Okamura, S.]] | [[Category: Okamura, S.]] | ||
[[Category: Parmeggiani, A.]] | [[Category: Parmeggiani, A.]] | ||
| - | [[Category: GNP]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: PUL]] | ||
[[Category: antibiotic]] | [[Category: antibiotic]] | ||
[[Category: elongation factor]] | [[Category: elongation factor]] | ||
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[[Category: translation elongation factor]] | [[Category: translation elongation factor]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:17:21 2008'' |
Revision as of 23:17, 30 March 2008
| |||||||
| , resolution 1.4Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , | ||||||
| Activity: | dGTPase, with EC number 3.1.5.1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
EF-TU COMPLEXED WITH A GTP ANALOG AND THE ANTIBIOTIC PULVOMYCIN
Overview
Pulvomycin inhibits protein synthesis by preventing the formation of the ternary complex between elongation factor Tu (EF-Tu) x GTP and aa-tRNA. In this work, the crystal structure of Thermus thermophilus EF-Tu x pulvomycin in complex with the GTP analogue guanylyl imino diphosphate (GDPNP) at 1.4 A resolution reveals an antibiotic binding site extending from the domain 1-3 interface to domain 2, overlapping the domain 1-2-3 junction. Pulvomycin binding interferes with the binding of the 3'-aminoacyl group, the acceptor stem, and 5' end of tRNA. Only part of pulvomycin overlaps the binding site of GE2270 A, a domain 2-bound antibiotic of a structure unrelated to pulvomycin, which also hinders aa-tRNA binding. The structure of the T. thermophilus EF-Tu x GDPNP x GE2270 A complex at 1.6 A resolution shows that GE2270 A interferes with the binding of the 3'-aminoacyl group and part of the acceptor stem of aa-tRNA but not with the 5' end. Both compounds, pulvomycin more markedly, hinder the correct positioning of domain 1 over domains 2 and 3 that characterizes the active form of EF-Tu, while they affect the domain 1 switch regions that control the EF-Tu x GDP/GTP transitions in different ways. This work reveals how two antibiotics with different structures and binding modes can employ a similar mechanism of action.
About this Structure
2C78 is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.
Reference
Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu., Parmeggiani A, Krab IM, Okamura S, Nielsen RC, Nyborg J, Nissen P, Biochemistry. 2006 Jun 6;45(22):6846-57. PMID:16734421
Page seeded by OCA on Mon Mar 31 02:17:21 2008
Categories: Single protein | Thermus thermophilus | DGTPase | Krab, I M. | Nielsen, R C. | Nissen, P. | Nyborg, J. | Okamura, S. | Parmeggiani, A. | Antibiotic | Elongation factor | Gtp-binding | Gtpase | Hydrolase | Nucleotide-binding | Phosphorylation | Protein biosynthesis | Protein synthesis | Translation elongation factor
