This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2rdl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:47, 16 March 2022) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2rdl.gif|left|200px]]
 
-
{{Structure
+
==Hamster Chymase 2==
-
|PDB= 2rdl |SIZE=350|CAPTION= <scene name='initialview01'>2rdl</scene>, resolution 2.500&Aring;
+
<StructureSection load='2rdl' size='340' side='right'caption='[[2rdl]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:Msu+Binding+Site+For+Residue+I+1'>AC1</scene>, <scene name='pdbsite=AC2:Msu+Binding+Site+For+Residue+J+1'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+A+246'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+B+246'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+A+247'>AC5</scene> and <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+B+247'>AC6</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
+
<table><tr><td colspan='2'>[[2rdl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Golden_hamster Golden hamster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDL FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
|GENE=
+
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0QE:CHLOROMETHANE'>0QE</scene>, <scene name='pdbligand=ALV:(2S)-2-AMINOPROPANE-1,1-DIOL'>ALV</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</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=2rdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdl OCA], [https://pdbe.org/2rdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdl RCSB], [https://www.ebi.ac.uk/pdbsum/2rdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdl ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Hamster Chymase 2'''
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
==Overview==
+
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdl_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=2rdl ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
Divergence of substrate specificity within the context of a common structural framework represents an important mechanism by which new enzyme activity naturally evolves. We present enzymological and x-ray structural data for hamster chymase-2 (HAM2) that provides a detailed explanation for the unusual hydrolytic specificity of this rodent alpha-chymase. In enzymatic characterization, hamster chymase-1 (HAM1) showed typical chymase proteolytic activity. In contrast, HAM2 exhibited atypical substrate specificity, cleaving on the carboxyl side of the P1 substrate residues Ala and Val, characteristic of elastolytic rather than chymotryptic specificity. The 2.5-A resolution crystal structure of HAM2 complexed to the peptidyl inhibitor MeOSuc-Ala-Ala-Pro-Ala-chloromethylketone revealed a narrow and shallow S1 substrate binding pocket that accommodated only a small hydrophobic residue (e.g. Ala or Val). The different substrate specificities of HAM2 and HAM1 are explained by changes in four S1 substrate site residues (positions 189, 190, 216, and 226). Of these, Asn(189), Val(190), and Val(216) form an easily identifiable triplet in all known rodent alpha-chymases that can be used to predict elastolytic specificity for novel chymase-like sequences. Phylogenetic comparison defines guinea pig and rabbit chymases as the closest orthologs to rodent alpha-chymases.
Divergence of substrate specificity within the context of a common structural framework represents an important mechanism by which new enzyme activity naturally evolves. We present enzymological and x-ray structural data for hamster chymase-2 (HAM2) that provides a detailed explanation for the unusual hydrolytic specificity of this rodent alpha-chymase. In enzymatic characterization, hamster chymase-1 (HAM1) showed typical chymase proteolytic activity. In contrast, HAM2 exhibited atypical substrate specificity, cleaving on the carboxyl side of the P1 substrate residues Ala and Val, characteristic of elastolytic rather than chymotryptic specificity. The 2.5-A resolution crystal structure of HAM2 complexed to the peptidyl inhibitor MeOSuc-Ala-Ala-Pro-Ala-chloromethylketone revealed a narrow and shallow S1 substrate binding pocket that accommodated only a small hydrophobic residue (e.g. Ala or Val). The different substrate specificities of HAM2 and HAM1 are explained by changes in four S1 substrate site residues (positions 189, 190, 216, and 226). Of these, Asn(189), Val(190), and Val(216) form an easily identifiable triplet in all known rodent alpha-chymases that can be used to predict elastolytic specificity for novel chymase-like sequences. Phylogenetic comparison defines guinea pig and rabbit chymases as the closest orthologs to rodent alpha-chymases.
-
==About this Structure==
+
Structural basis for elastolytic substrate specificity in rodent alpha-chymases.,Kervinen J, Abad M, Crysler C, Kolpak M, Mahan AD, Masucci JA, Bayoumy S, Cummings MD, Yao X, Olson M, de Garavilla L, Kuo L, Deckman I, Spurlino J J Biol Chem. 2008 Jan 4;283(1):427-36. Epub 2007 Oct 31. PMID:17981788<ref>PMID:17981788</ref>
-
2RDL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mesocricetus_auratus Mesocricetus auratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDL OCA].
+
-
 
+
-
==Reference==
+
-
Structural basis for elastolytic substrate specificity in rodent alpha-chymases., Kervinen J, Abad M, Crysler C, Kolpak M, Mahan AD, Masucci JA, Bayoumy S, Cummings MD, Yao X, Olson M, de Garavilla L, Kuo L, Deckman I, Spurlino J, J Biol Chem. 2008 Jan 4;283(1):427-36. Epub 2007 Oct 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17981788 17981788]
+
-
[[Category: Mesocricetus auratus]]
+
-
[[Category: Single protein]]
+
-
[[Category: Abad, M.]]
+
-
[[Category: Kervinen, J.]]
+
-
[[Category: Spurlino, J.]]
+
-
[[Category: SO4]]
+
-
[[Category: chymase 2]]
+
-
[[Category: hamster]]
+
-
[[Category: hydrolase]]
+
-
[[Category: serine protease]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:35:03 2008''
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2rdl" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Golden hamster]]
 +
[[Category: Large Structures]]
 +
[[Category: Abad, M]]
 +
[[Category: Kervinen, J]]
 +
[[Category: Spurlino, J]]
 +
[[Category: Chymase 2]]
 +
[[Category: Hydrolase-hydrolase inhibitor complex]]
 +
[[Category: Serine protease]]

Current revision

Hamster Chymase 2

PDB ID 2rdl

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/2rdl"
Personal tools