1dff

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:53, 7 February 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dff.gif|left|200px]]<br /><applet load="1dff" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dff, resolution 2.88&Aring;" />
 
-
'''PEPTIDE DEFORMYLASE'''<br />
 
-
==Overview==
+
==PEPTIDE DEFORMYLASE==
-
Protein synthesis in bacteria involves the formylation and deformylation, of the N-terminal methionine. As eukaryotic organisms differ in their, protein biosynthetic mechanisms, peptide deformylase, the bacterial enzyme, responsible for deformylation, represents a potential target for, antibiotic studies. Here we report the crystallization and 2.9 A X-ray, structure solution of the zinc containing Escherichia coli peptide, deformylase. While the primary sequence, tertiary structure, and use of, coordinated cysteine suggest that E. coli deformylase belongs to a new, subfamily of metalloproteases, the environment around the metal appears to, have strong geometric similarity to the active sites of the thermolysin, family. This suggests a possible similarity in their hydrolytic, mechanisms. Another important issue is the origin of the enzyme's, specificity for N-formylated over N-acetylated substrates. Based on the, structure, the specificity appears to result from hydrogen-bonding, interactions which orient the substrate for cleavage, and steric factors, which physically limit the size of the N-terminal carbonyl group.
+
<StructureSection load='1dff' size='340' side='right'caption='[[1dff]], [[Resolution|resolution]] 2.88&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1dff]] is a 1 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=1DFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DFF FirstGlance]. <br>
-
1DFF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Known structural/functional Site: <scene name='pdbsite=CAT:Zn+Binding+Site'>CAT</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFF OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.88&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dff OCA], [https://pdbe.org/1dff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dff RCSB], [https://www.ebi.ac.uk/pdbsum/1dff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dff ProSAT]</span></td></tr>
-
Crystal structure of the Escherichia coli peptide deformylase., Chan MK, Gong W, Rajagopalan PT, Hao B, Tsai CM, Pei D, Biochemistry. 1997 Nov 11;36(45):13904-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9374869 9374869]
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI] 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.[HAMAP-Rule:MF_00163]
 +
== Evolutionary Conservation ==
 +
[[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/df/1dff_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1dff ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Formylmethionine deformylase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Chan MK]]
-
[[Category: Chan, M.K.]]
+
[[Category: Gong W]]
-
[[Category: Gong, W.]]
+
[[Category: Hao B]]
-
[[Category: Hao, B.]]
+
[[Category: Pei D]]
-
[[Category: Pei, D.]]
+
[[Category: Rajagopalan PTR]]
-
[[Category: Rajagopalan, P.T.R.]]
+
[[Category: Tsai CM]]
-
[[Category: Tsai, C.M.]]
+
-
[[Category: ZN]]
+
-
[[Category: hydrolase]]
+
-
[[Category: zinc metalloprotease]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:35:29 2008''
+

Current revision

PEPTIDE DEFORMYLASE

PDB ID 1dff

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/1dff"
Personal tools