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2bvn

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E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa

Structural highlights

2bvn is a 2 chain structure with sequence from Escherichia coli BL21. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EFTU2_ECOLI This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P. Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics. J Biol Chem. 2006 Feb 3;281(5):2893-900. Epub 2005 Oct 28. PMID:16257965 doi:10.1074/jbc.M505951200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bvn"

@@ Line 3: / Line 3: @@
 <StructureSection load='2bvn' size='340' side='right'caption='[[2bvn]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2bvn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2bvn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21 Escherichia coli BL21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ENX:ENACYLOXIN+IIA'>ENX</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-synthesizing_GTPase Protein-synthesizing GTPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.5.3 3.6.5.3] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ENX:ENACYLOXIN+IIA'>ENX</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvn OCA], [https://pdbe.org/2bvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvn RCSB], [https://www.ebi.ac.uk/pdbsum/2bvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvn ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/EFTU2_ECOLI EFTU2_ECOLI] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118]  May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Escherichia coli BL21]]
 [[Category: Large Structures]]
-[[Category: Protein-synthesizing GTPase]]
+[[Category: Dahlberg C]]
-[[Category: Dahlberg, C]]
+[[Category: Krab IM]]
-[[Category: Krab, I M]]
+[[Category: Nielsen RC]]
-[[Category: Nielsen, R C]]
+[[Category: Nissen P]]
-[[Category: Nissen, P]]
+[[Category: Nyborg J]]
-[[Category: Nyborg, J]]
+[[Category: Parmeggiani A]]
-[[Category: Parmeggiani, A]]
+[[Category: Watanabe T]]
-[[Category: Watanabe, T]]
-[[Category: Antibiotic]]
-[[Category: Elongation factor]]
-[[Category: Gtp-binding]]
-[[Category: Gtpase]]
-[[Category: Phosphorylation]]
-[[Category: Translation]]

2bvn

From Proteopedia

Current revision

E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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