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.


1ru4

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:27, 1 May 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ru4.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of pectate lyase Pel9A==
-
|PDB= 1ru4 |SIZE=350|CAPTION= <scene name='initialview01'>1ru4</scene>, resolution 1.60&Aring;
+
<StructureSection load='1ru4' size='340' side='right'caption='[[1ru4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>
+
<table><tr><td colspan='2'>[[1ru4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_chrysanthemi Dickeya chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RU4 FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-
|GENE= PelL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=556 Erwinia chrysanthemi])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ru4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ru4 OCA], [https://pdbe.org/1ru4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ru4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ru4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ru4 ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ru4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ru4 OCA], [http://www.ebi.ac.uk/pdbsum/1ru4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ru4 RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/PLYL_DICD3 PLYL_DICD3] Presents an endo-cleaving activity on polygalacturonate or partially methylated pectin. Is effective in the maceration of plant tissue, and has an important role in soft-rot disease. Is 280-fold less active against polygalacturonate than the major pectate lyase PelB. When assayed on polygalacturonate, PelL releases oligogalacturonates of different sizes; upon prolonged incubation, PelL degrades the primary products to unsaturated tetramer and pentamer in addition to unsaturated dimer and trimer. When assayed on oligogalacturonates (degrees of polymerization of 2 to 8), it preferentially forms unsaturated tetramer, and displays the highest activity on the octamer.<ref>PMID:10368144</ref> <ref>PMID:8577252</ref>
-
 
+
== Evolutionary Conservation ==
-
'''Crystal structure of pectate lyase Pel9A'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ru/1ru4_consurf.spt"</scriptWhenChecked>
-
The "family 9 polysaccharide lyase" pectate lyase L (Pel9A) from Erwinia chrysanthemi comprises a 10-coil parallel beta-helix domain with distinct structural features including an asparagine ladder and aromatic stack at novel positions within the superhelical structure. Pel9A has a single high affinity calcium-binding site strikingly similar to the "primary" calcium-binding site described previously for the family Pel1A pectate lyases, and there is strong evidence for a common second calcium ion that binds between enzyme and substrate in the "Michaelis" complex. Although the primary calcium ion binds substrate in subsite -1, it is the second calcium ion, whose binding site is formed by the coming together of enzyme and substrate, that facilitates abstraction of the C5 proton from the sacharride in subsite +1. The role of the second calcium is to withdraw electrons from the C6 carboxylate of the substrate, thereby acidifying the C5 proton facilitating its abstraction and resulting in an E1cb-like anti-beta-elimination mechanism. The active site geometries and mechanism of Pel1A and Pel9A are closely similar, but the catalytic base is a lysine in the Pel9A enzymes as opposed to an arginine in the Pel1A enzymes.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1RU4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RU4 OCA].
+
</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=1ru4 ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
== References ==
-
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi., Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW, J Biol Chem. 2004 Mar 5;279(10):9139-45. Epub 2003 Dec 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14670977 14670977]
+
<references/>
-
[[Category: Erwinia chrysanthemi]]
+
__TOC__
-
[[Category: Pectate lyase]]
+
</StructureSection>
-
[[Category: Single protein]]
+
[[Category: Dickeya chrysanthemi]]
-
[[Category: Hugouvieux-Cotte-Pattat, N.]]
+
[[Category: Large Structures]]
-
[[Category: Jenkins, J.]]
+
[[Category: Hugouvieux-Cotte-Pattat N]]
-
[[Category: Pickersgill, R W.]]
+
[[Category: Jenkins J]]
-
[[Category: Shevchik, V E.]]
+
[[Category: Pickersgill RW]]
-
[[Category: parallel beta-helix]]
+
[[Category: Shevchik VE]]
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:33:02 2008''
+

Current revision

Crystal structure of pectate lyase Pel9A

PDB ID 1ru4

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/1ru4"
Personal tools