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.


2i4n

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:01, 21 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2i4n.jpg|left|200px]]
 
-
{{Structure
+
==Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with CysAMS==
-
|PDB= 2i4n |SIZE=350|CAPTION= <scene name='initialview01'>2i4n</scene>, resolution 2.85&Aring;
+
<StructureSection load='2i4n' size='340' side='right'caption='[[2i4n]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=5CA:5&#39;-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE'>5CA</scene>
+
<table><tr><td colspan='2'>[[2i4n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I4N FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline--tRNA_ligase Proline--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.15 6.1.1.15] </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]] 2.85&#8491;</td></tr>
-
|GENE= proS,RPA2928 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1076 Rhodopseudomonas palustris])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CA:5-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE'>5CA</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=2i4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i4n OCA], [https://pdbe.org/2i4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i4n RCSB], [https://www.ebi.ac.uk/pdbsum/2i4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i4n ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2i4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i4n OCA], [http://www.ebi.ac.uk/pdbsum/2i4n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2i4n RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/SYP_RHOPA SYP_RHOPA] Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process cysteine. The misacylated Cys-tRNA(Pro) is not edited by ProRS.[HAMAP-Rule:MF_01570]
 +
== 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/i4/2i4n_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=2i4n ConSurf].
 +
<div style="clear:both"></div>
-
'''Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with CysAMS'''
+
==See Also==
-
 
+
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins YbaK and ProX. Here, we describe crystal structures of two bacterial ProRSs from the pathogen Enterococcus faecalis, which possesses an editing domain, and from Rhodopseudomonas palustris, which does not. We compare the overall structure and binding mode of ATP and prolyl-adenylate with those of the archael/eukaryote-type ProRS from Thermus thermophilus. Although structurally more homologous to YbaK, which preferentially hydrolyzes Cys-tRNA(Pro), the editing domain of E. faecalis ProRS possesses key elements similar to ProX, with which it shares the activity of hydrolyzing Ala-tRNA(Pro). The structures give insight into the complex evolution of ProRSs, the mechanism of editing, and structural differences between prokaryotic- and eukaryotic-type ProRSs that can be exploited for antibiotic design.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
2I4N is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I4N OCA].
+
-
 
+
-
==Reference==
+
-
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain., Crepin T, Yaremchuk A, Tukalo M, Cusack S, Structure. 2006 Oct;14(10):1511-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17027500 17027500]
+
-
[[Category: Proline--tRNA ligase]]
+
[[Category: Rhodopseudomonas palustris]]
[[Category: Rhodopseudomonas palustris]]
-
[[Category: Single protein]]
+
[[Category: Crepin T]]
-
[[Category: Crepin, T.]]
+
[[Category: Cusack S]]
-
[[Category: Cusack, S.]]
+
[[Category: Tukalo M]]
-
[[Category: Tukalo, M.]]
+
[[Category: Yaremchuk A]]
-
[[Category: Yaremchuk, A.]]
+
-
[[Category: alpha beta]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:39:36 2008''
+

Current revision

Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with CysAMS

PDB ID 2i4n

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/2i4n"
Personal tools