1p3e

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1p3e" size="450" color="white" frame="true" align="right" spinBox="true" caption="1p3e, resolution 1.72&Aring;" /> '''Structure of Glu end...)
Current revision (07:11, 30 October 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1p3e.gif|left|200px]]<br /><applet load="1p3e" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1p3e, resolution 1.72&Aring;" />
 
-
'''Structure of Glu endopeptidase in complex with MPD'''<br />
 
-
==Overview==
+
==Structure of Glu endopeptidase in complex with MPD==
-
Extracellular glutamyl endopeptidase from Bacillus intermedius (BIEP) is a, chymotrypsin-like serine protease which cleaves the peptide bond on the, carboxyl side of glutamic acid. Its three-dimensional structure was, determined for C222(1) and C2 crystal forms of BIEP to 1.5 and 1.75 A, resolution, respectively. The topology of BIEP diverges from the most, common chymotrypsin architecture, because one of the domains consists of a, beta-sandwich consisting of two antiparallel beta-sheets and two helices., In the C2 crystals, a 2-methyl-2,4-pentanediol (MPD) molecule was found in, the substrate binding site, mimicking a glutamic acid. This enabled the, identification of the residues involved in the substrate recognition. The, presence of the MPD molecule causes a change in the active site; the, interaction between two catalytic residues (His47 and Ser171) is, disrupted. The N-terminal end of the enzyme is involved in the formation, of the substrate binding pocket. This indicates a direct relation between, zymogen activation and substrate charge compensation.
+
<StructureSection load='1p3e' size='340' side='right'caption='[[1p3e]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1p3e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_intermedius Bacillus intermedius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P3E FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=1p3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p3e OCA], [https://pdbe.org/1p3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p3e RCSB], [https://www.ebi.ac.uk/pdbsum/1p3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p3e ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q9EXR9_BACIN Q9EXR9_BACIN]
 +
== 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/p3/1p3e_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=1p3e ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Extracellular glutamyl endopeptidase from Bacillus intermedius (BIEP) is a chymotrypsin-like serine protease which cleaves the peptide bond on the carboxyl side of glutamic acid. Its three-dimensional structure was determined for C222(1) and C2 crystal forms of BIEP to 1.5 and 1.75 A resolution, respectively. The topology of BIEP diverges from the most common chymotrypsin architecture, because one of the domains consists of a beta-sandwich consisting of two antiparallel beta-sheets and two helices. In the C2 crystals, a 2-methyl-2,4-pentanediol (MPD) molecule was found in the substrate binding site, mimicking a glutamic acid. This enabled the identification of the residues involved in the substrate recognition. The presence of the MPD molecule causes a change in the active site; the interaction between two catalytic residues (His47 and Ser171) is disrupted. The N-terminal end of the enzyme is involved in the formation of the substrate binding pocket. This indicates a direct relation between zymogen activation and substrate charge compensation.
-
==About this Structure==
+
The crystal structure of glutamyl endopeptidase from Bacillus intermedius reveals a structural link between zymogen activation and charge compensation.,Meijers R, Blagova EV, Levdikov VM, Rudenskaya GN, Chestukhina GG, Akimkina TV, Kostrov SV, Lamzin VS, Kuranova IP Biochemistry. 2004 Mar 16;43(10):2784-91. PMID:15005613<ref>PMID:15005613</ref>
-
1P3E is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_intermedius Bacillus intermedius] with MPD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1P3E OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
The crystal structure of glutamyl endopeptidase from Bacillus intermedius reveals a structural link between zymogen activation and charge compensation., Meijers R, Blagova EV, Levdikov VM, Rudenskaya GN, Chestukhina GG, Akimkina TV, Kostrov SV, Lamzin VS, Kuranova IP, Biochemistry. 2004 Mar 16;43(10):2784-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15005613 15005613]
+
</div>
 +
<div class="pdbe-citations 1p3e" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Bacillus intermedius]]
[[Category: Bacillus intermedius]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Akimkina, T.V.]]
+
[[Category: Akimkina TV]]
-
[[Category: Blagova, E.V.]]
+
[[Category: Blagova EV]]
-
[[Category: Chestukhina, G.G.]]
+
[[Category: Chestukhina GG]]
-
[[Category: Kostrov, S.V.]]
+
[[Category: Kostrov SV]]
-
[[Category: Kuranova, I.P.]]
+
[[Category: Kuranova IP]]
-
[[Category: Lamzin, V.S.]]
+
[[Category: Lamzin VS]]
-
[[Category: Levdikov, V.M.]]
+
[[Category: Levdikov VM]]
-
[[Category: Meijers, R.]]
+
[[Category: Meijers R]]
-
[[Category: Rudenskaya, G.N.]]
+
[[Category: Rudenskaya GN]]
-
[[Category: MPD]]
+
-
[[Category: glu specific]]
+
-
[[Category: serine protease]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:54:55 2007''
+

Current revision

Structure of Glu endopeptidase in complex with MPD

PDB ID 1p3e

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/1p3e"
Personal tools