1lry

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:35, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1lry.gif|left|200px]]
 
-
{{Structure
+
==Crystal Structure of P. aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin==
-
|PDB= 1lry |SIZE=350|CAPTION= <scene name='initialview01'>1lry</scene>, resolution 2.6&Aring;
+
<StructureSection load='1lry' size='340' side='right'caption='[[1lry]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>
+
<table><tr><td colspan='2'>[[1lry]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRY FirstGlance]. <br>
-
|ACTIVITY= [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]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lry OCA], [https://pdbe.org/1lry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lry RCSB], [https://www.ebi.ac.uk/pdbsum/1lry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lry ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure of P. aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/DEF_PSEAE DEF_PSEAE] 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).
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lry_consurf.spt"</scriptWhenChecked>
-
1LRY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRY OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents., Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V, J Mol Biol. 2002 Jul 26;320(5):951-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12126617 12126617]
+
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lry ConSurf].
-
[[Category: Peptide deformylase]]
+
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
-
[[Category: Single protein]]
+
[[Category: Blanc V]]
-
[[Category: Blanc, V.]]
+
[[Category: Chevrier M]]
-
[[Category: Chevrier, M.]]
+
[[Category: Dupuy A]]
-
[[Category: Dupuy, A.]]
+
[[Category: Famechon A]]
-
[[Category: Famechon, A.]]
+
[[Category: Giglione C]]
-
[[Category: Giglione, C.]]
+
[[Category: Gil P]]
-
[[Category: Gil, P.]]
+
[[Category: Guilloteau J-P]]
-
[[Category: Guilloteau, J P.]]
+
[[Category: Mathieu M]]
-
[[Category: Mathieu, M.]]
+
[[Category: Meinnel T]]
-
[[Category: Meinnel, T.]]
+
[[Category: Mikol V]]
-
[[Category: Mikol, V.]]
+
-
[[Category: BB2]]
+
-
[[Category: ZN]]
+
-
[[Category: actinonin]]
+
-
[[Category: inhibition]]
+
-
[[Category: polypeptide deformylase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:34:25 2008''
+

Current revision

Crystal Structure of P. aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin

PDB ID 1lry

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1lry"
Personal tools