1y79

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:55, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1y79.gif|left|200px]]<br /><applet load="1y79" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1y79, resolution 2.00&Aring;" />
 
-
'''Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a Peptidic Inhibitor'''<br />
 
-
==Overview==
+
==Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a Peptidic Inhibitor==
-
Dcp from Escherichia coli is a 680 residue cytoplasmic peptidase, which shows a strict dipeptidyl carboxypeptidase activity. Although Dcp had been assigned to the angiotensin I-converting enzymes (ACE) due to blockage by typical ACE inhibitors, it is currently grouped into the M3 family of mono zinc peptidases, which also contains the endopeptidases neurolysin and thimet oligopeptidase (TOP). We have cloned, expressed, purified, and crystallized Dcp in the presence of an octapeptide "inhibitor", and have determined its 2.0A crystal structure using MAD methods. The analysis revealed that Dcp consists of two half shell-like subdomains, which enclose an almost closed two-chamber cavity. In this cavity, two dipeptide products presumably generated by Dcp cleavage of the octapeptide bind to the thermolysin-like active site fixed to side-chains, which are provided by both subdomains. In particular, an Arg side-chain backed by a Glu residue, together with two Tyr phenolic groups provide a charged anchor for fixing the C-terminal carboxylate group of the P2' residue of a bound substrate, explaining the strict dipeptidyl carboxypeptidase specificity of Dcp. Tetrapeptidic substrates are fixed only via their main-chain functions from P2 to P2', suggesting a broad residue specificity for Dcp. Both subdomains exhibit very similar chain folds as the equivalent but abducted subdomains of neurolysin and TOP. Therefore, this "product-bound" Dcp structure seems to represent the inhibitor/substrate-bound "closed" form of the M3 peptidases, generated from the free "open" substrate-accessible form by a hinge-bending mechanism. A similar mechanism has recently been demonstrated experimentally for ACE2.
+
<StructureSection load='1y79' size='340' side='right'caption='[[1y79]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1y79]] 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=1Y79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y79 FirstGlance]. <br>
-
1Y79 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>, <scene name='pdbligand=LYS:'>LYS</scene> and <scene name='pdbligand=GLY:'>GLY</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Peptidyl-dipeptidase_Dcp Peptidyl-dipeptidase Dcp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.15.5 3.4.15.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y79 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&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>, <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=1y79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y79 OCA], [https://pdbe.org/1y79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y79 RCSB], [https://www.ebi.ac.uk/pdbsum/1y79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y79 ProSAT]</span></td></tr>
-
Crystal structure of the E. coli dipeptidyl carboxypeptidase Dcp: further indication of a ligand-dependent hinge movement mechanism., Comellas-Bigler M, Lang R, Bode W, Maskos K, J Mol Biol. 2005 May 27;349(1):99-112. Epub 2005 Mar 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15876371 15876371]
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DCP_ECOLI DCP_ECOLI] Removes dipeptides from the C-termini of N-blocked tripeptides, tetrapeptides and larger peptides.
 +
== 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/y7/1y79_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=1y79 ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Peptidyl-dipeptidase Dcp]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Bode W]]
-
[[Category: Bode, W.]]
+
[[Category: Comellas-Bigler M]]
-
[[Category: Comellas-Bigler, M.]]
+
[[Category: Lang R]]
-
[[Category: Lang, R.]]
+
[[Category: Maskos K]]
-
[[Category: Maskos, K.]]
+
-
[[Category: GLY]]
+
-
[[Category: LYS]]
+
-
[[Category: ZN]]
+
-
[[Category: hinge bending; peptidyl dipeptidase; carboxypeptidase; dcp; neurolysin; ace]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:02:24 2008''
+

Current revision

Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a Peptidic Inhibitor

PDB ID 1y79

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/1y79"
Personal tools