This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1y6h

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 18:32, 10 September 2015

Crystal structure of LIPDF

Structural highlights

1y6h is a 2 chain structure with sequence from "leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919. This structure supersedes the now removed PDB entry 1rn5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	def ("Leptospira icteroides" Noguchi 1919)
Activity:	Peptide deformylase, with EC number 3.5.1.88
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[DEF_LEPIN] 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

Peptide deformylase (PDF), which is essential for normal growth of bacteria but not for higher organisms, is explored as an attractive target for developing novel antibiotics. Here, we present the crystal structure of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our knowledge, this is the first crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66-76) near the active-site pocket adopts "closed" or "open" conformations in the two monomers forming the dimer. In the closed subunit, the CD-loop and residue Arg109 block the entry of the substrate-binding pocket, while the active-site pocket of the open subunit is occupied by the C-terminal tail from the neighbouring molecule. Moreover, a formate group, as one product of deformylisation, is observed bound with the active-site zinc ion. LiPDF displays significant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs.

Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans.,Zhou Z, Song X, Li Y, Gong W J Mol Biol. 2004 May 21;339(1):207-15. PMID:15123432^[1]

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

References

↑ Zhou Z, Song X, Li Y, Gong W. Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans. J Mol Biol. 2004 May 21;339(1):207-15. PMID:15123432 doi:10.1016/j.jmb.2004.03.045

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/1y6h"

@@ Line 2: / Line 2: @@
 <StructureSection load='1y6h' size='340' side='right' caption='[[1y6h]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 Leptospira interrogans])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 "Leptospira icteroides" Noguchi 1919])</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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h 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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://pdbe.org/1y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1y6h" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Leptospira interrogans]]
+[[Category: Leptospira icteroides noguchi 1919]]
 [[Category: Peptide deformylase]]
 [[Category: Gong, W]]

1y6h

From Proteopedia

Revision as of 18:32, 10 September 2015

Crystal structure of LIPDF

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox