3g6n

From Proteopedia

(Difference between revisions)

Revision as of 08:03, 5 December 2018

Crystal structure of an EfPDF complex with Met-Ala-Ser

Structural highlights

3g6n is a 4 chain structure with sequence from Atcc 19434. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3cmd
Activity:	Peptide deformylase, with EC number 3.5.1.88
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[Q842S4_ENTFC] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]

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

PDF (peptide deformylase) plays a critical role in the production of mature proteins by removing the N-formyl polypeptide of nascent proteins in the prokaryote cell system. This protein is essential for bacterial growth, making it an attractive target for the design of new antibiotics. Accordingly, PDF has been evaluated as a drug target; however, architectural mechanism studies of PDF have not yet fully elucidated its molecular function. We recently reported the crystal structure of PDF produced by Enterococcus faecium [K.H. Nam, J.I. Ham, A. Priyadarshi, E.E. Kim, N. Chung, K.Y. Hwang, "Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure", Proteins 74 (2009) 261-265]. Here, we present the crystal structure of the EfPDF complex with MAS (Met-Ser-Ala), thereby not only delineating the architectural mechanism for the recognition of mimic-peptides by N-terminal cleaved expression peptide, but also suggesting possible targets for rational design of antibacterial drugs. In addition to their implications for drug design, these structural studies will facilitate elucidation of the architectural mechanism responsible for the peptide recognition of PDF.

Crystal structure of an EfPDF complex with Met-Ala-Ser based on crystallographic packing.,Nam KH, Kim KH, Kim EE, Hwang KY Biochem Biophys Res Commun. 2009 Apr 17;381(4):630-3. Epub 2009 Feb 26. PMID:19249287^[1]

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

References

↑ Nam KH, Kim KH, Kim EE, Hwang KY. Crystal structure of an EfPDF complex with Met-Ala-Ser based on crystallographic packing. Biochem Biophys Res Commun. 2009 Apr 17;381(4):630-3. Epub 2009 Feb 26. PMID:19249287 doi:10.1016/j.bbrc.2009.02.113

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3g6n"

@@ Line 1: / Line 1: @@
 ==Crystal structure of an EfPDF complex with Met-Ala-Ser==
 <StructureSection load='3g6n' size='340' side='right' caption='[[3g6n]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cmd|3cmd]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://pdbe.org/3g6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6n OCA], [http://pdbe.org/3g6n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g6n RCSB], [http://www.ebi.ac.uk/pdbsum/3g6n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g6n ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/3g6n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/3g6n_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

3g6n

From Proteopedia

Revision as of 08:03, 5 December 2018

Crystal structure of an EfPDF complex with Met-Ala-Ser

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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