1jym

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:52, 30 October 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1jym.gif|left|200px]]
 
-
{{Structure
+
==Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design==
-
|PDB= 1jym |SIZE=350|CAPTION= <scene name='initialview01'>1jym</scene>, resolution 2.80&Aring;
+
<StructureSection load='1jym' size='340' side='right'caption='[[1jym]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CO:COBALT (II) ION'>CO</scene>
+
<table><tr><td colspan='2'>[[1jym]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JYM FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-
|GENE= PDF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5833 Plasmodium falciparum])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1jym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jym OCA], [https://pdbe.org/1jym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jym RCSB], [https://www.ebi.ac.uk/pdbsum/1jym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jym ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/Q8I372_PLAF7 Q8I372_PLAF7]
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jy/1jym_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1jym ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
Peptide deformylase catalyzes the deformylation reaction of the amino terminal fMet residue of newly synthesized proteins in bacteria, and most likely in Plasmodium falciparum, and has therefore been identified as a potential antibacterial and antimalarial drug target. The structure of P. falciparum peptide deformylase, determined at 2.8 A resolution with ten subunits per asymmetric unit, is similar to the bacterial enzyme with the residues involved in catalysis, the position of the bound metal ion, and a catalytically important water structurally conserved between the two enzymes. However, critical differences in the substrate binding region explain the poor affinity of E. coli deformylase inhibitors and substrates toward the Plasmodium enzyme. The Plasmodium structure serves as a guide for designing novel antimalarials.
Peptide deformylase catalyzes the deformylation reaction of the amino terminal fMet residue of newly synthesized proteins in bacteria, and most likely in Plasmodium falciparum, and has therefore been identified as a potential antibacterial and antimalarial drug target. The structure of P. falciparum peptide deformylase, determined at 2.8 A resolution with ten subunits per asymmetric unit, is similar to the bacterial enzyme with the residues involved in catalysis, the position of the bound metal ion, and a catalytically important water structurally conserved between the two enzymes. However, critical differences in the substrate binding region explain the poor affinity of E. coli deformylase inhibitors and substrates toward the Plasmodium enzyme. The Plasmodium structure serves as a guide for designing novel antimalarials.
-
==About this Structure==
+
Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design.,Kumar A, Nguyen KT, Srivathsan S, Ornstein B, Turley S, Hirsh I, Pei D, Hol WG Structure. 2002 Mar;10(3):357-67. PMID:12005434<ref>PMID:12005434</ref>
-
1JYM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JYM OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design., Kumar A, Nguyen KT, Srivathsan S, Ornstein B, Turley S, Hirsh I, Pei D, Hol WG, Structure. 2002 Mar;10(3):357-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12005434 12005434]
+
</div>
-
[[Category: Formylmethionine deformylase]]
+
<div class="pdbe-citations 1jym" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Plasmodium falciparum]]
[[Category: Plasmodium falciparum]]
-
[[Category: Single protein]]
+
[[Category: Hirsh I]]
-
[[Category: Hirsh, I.]]
+
[[Category: Hol WGJ]]
-
[[Category: Hol, W G.J.]]
+
[[Category: Kumar A]]
-
[[Category: Kumar, A.]]
+
[[Category: Nguyen KT]]
-
[[Category: Nguyen, K T.]]
+
[[Category: Ornstein B]]
-
[[Category: Ornstein, B.]]
+
[[Category: Pei D]]
-
[[Category: Pei, D.]]
+
[[Category: Srivathsan S]]
-
[[Category: Srivathsan, S.]]
+
[[Category: Turley S]]
-
[[Category: Turley, S.]]
+
-
[[Category: CO]]
+
-
[[Category: deformylation]]
+
-
[[Category: malaria]]
+
-
[[Category: metalloenzyme]]
+
-
[[Category: pdf]]
+
-
[[Category: plasmodium]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:10:12 2008''
+

Current revision

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

PDB ID 1jym

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/1jym"
Personal tools