1ob5
From Proteopedia
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|PDB= 1ob5 |SIZE=350|CAPTION= <scene name='initialview01'>1ob5</scene>, resolution 3.10Å | |PDB= 1ob5 |SIZE=350|CAPTION= <scene name='initialview01'>1ob5</scene>, resolution 3.10Å | ||
|SITE= <scene name='pdbsite=AC1:Enx+Binding+Site+For+Chain+E'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Enx+Binding+Site+For+Chain+E'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5'-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5'-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5'-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=ENX:ENACYLOXIN+IIA'>ENX</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MAD:6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE'>MAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PHA:PHENYLALANINAL'>PHA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5'-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/ | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-synthesizing_GTPase Protein-synthesizing GTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.5.3 3.6.5.3] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ob5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ob5 OCA], [http://www.ebi.ac.uk/pdbsum/1ob5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ob5 RCSB]</span> | ||
}} | }} | ||
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Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics., Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P, J Biol Chem. 2006 Feb 3;281(5):2893-900. Epub 2005 Oct 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16257965 16257965] | Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics., Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P, J Biol Chem. 2006 Feb 3;281(5):2893-900. Epub 2005 Oct 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16257965 16257965] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| + | [[Category: Protein-synthesizing GTPase]] | ||
[[Category: Thermus aquaticus]] | [[Category: Thermus aquaticus]] | ||
| - | [[Category: Transferred entry: 3 6.5 3]] | ||
[[Category: Dahlberg, C.]] | [[Category: Dahlberg, C.]] | ||
[[Category: Nielsen, R C.]] | [[Category: Nielsen, R C.]] | ||
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[[Category: Nyborg, J.]] | [[Category: Nyborg, J.]] | ||
[[Category: Parmeggiani, A.]] | [[Category: Parmeggiani, A.]] | ||
| - | [[Category: C]] | ||
| - | [[Category: ENX]] | ||
| - | [[Category: GNP]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: PHA]] | ||
[[Category: gtp-binding]] | [[Category: gtp-binding]] | ||
[[Category: gtpase]] | [[Category: gtpase]] | ||
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[[Category: translation elongation factor]] | [[Category: translation elongation factor]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:42:37 2008'' |
Revision as of 19:42, 30 March 2008
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| , resolution 3.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , , , , , , , , , , , , , , , | ||||||
| Activity: | Protein-synthesizing GTPase, with EC number 3.6.5.3 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T. AQUATICUS ELONGATION FACTOR EF-TU COMPLEXED WITH THE ANTIBIOTIC ENACYLOXIN IIA, A GTP ANALOG, AND PHE-TRNA
Overview
Elongation factor (EF-) Tu.GTP is the carrier of aminoacyl-tRNA to the programmed ribosome. Enacyloxin IIa inhibits bacterial protein synthesis by hindering the release of EF-Tu.GDP from the ribosome. The crystal structure of the Escherichia coli EF-Tu.guanylyl iminodiphosphate (GDPNP).enacyloxin IIa complex at 2.3 A resolution presented here reveals the location of the antibiotic at the interface of domains 1 and 3. The binding site overlaps that of kirromycin, an antibiotic with a structure that is unrelated to enacyloxin IIa but that also inhibits EF-Tu.GDP release. As one of the major differences, the enacyloxin IIa tail borders a hydrophobic pocket that is occupied by the longer tail of kirromycin, explaining the higher binding affinity of the latter. EF-Tu.GDPNP.enacyloxin IIa shows a disordered effector region that in the Phe-tRNAPhe.EF-Tu (Thermus aquaticus).GDPNP.enacyloxin IIa complex, solved at 3.1 A resolution, is stabilized by the interaction with tRNA. This work clarifies the structural background of the action of enacyloxin IIa and compares its properties with those of kirromycin, opening new perspectives for structure-guided design of novel antibiotics.
About this Structure
1OB5 is a Protein complex structure of sequences from Thermus aquaticus. Full crystallographic information is available from OCA.
Reference
Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics., Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P, J Biol Chem. 2006 Feb 3;281(5):2893-900. Epub 2005 Oct 28. PMID:16257965
Page seeded by OCA on Sun Mar 30 22:42:37 2008
