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.


2ip6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2ip6" size="350" color="white" frame="true" align="right" spinBox="true" caption="2ip6, resolution 1.35&Aring;" /> '''Crystal structure of...)
Current revision (13:53, 13 March 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ip6.jpg|left|200px]]<br /><applet load="2ip6" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2ip6, resolution 1.35&Aring;" />
 
-
'''Crystal structure of PedB'''<br />
 
-
==Overview==
+
==Crystal structure of PedB==
-
BACKGROUND: Pediocin-like bacteriocins, ribosomally-synthesized, antimicrobial peptides, are generally coexpressed with cognate immunity, proteins in order to protect the bacteriocin-producer from its own, bacteriocin. As a step for understanding the mode of action of immunity, proteins, we determined the crystal structure of PedB, a pediocin-like, immunity protein conferring immunity to pediocin PP-1. RESULTS: The 1.6 A, crystal structure of PedB reveals that PedB consists of an antiparallel, four-helix bundle with a flexible C-terminal end. PedB shows structural, similarity to an immunity protein against enterocin A (EntA-im) but some, disparity to an immunity protein against carnobacteriocin B2 (ImB2) in, both the C-terminal conformation and the local structure constructed by, alpha3, alpha4, and their connecting loop. Structure-inspired mutational, studies reveal that deletion of the last seven residues of the C-terminus, of PedB almost abolished its immunity activity. CONCLUSION: The fact that, PedB, EntA-im, and ImB2 share a four-helix bundle structure strongly, suggests the structural conservation of this motif in the pediocin-like, immunity proteins. The significant difference in the core structure and, the C-terminal conformation provides a structural basis for the, classification of pediocin-like immunity proteins. Our mutational study, using C-terminal-shortened PedBs and the investigation of primary sequence, of the C-terminal region, propose that several polar or charged residues, in the extreme C-terminus of PedB which is crucial for the immunity are, involved in the specific recognition of pediocin PP-1.
+
<StructureSection load='2ip6' size='340' side='right'caption='[[2ip6]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[2ip6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pediococcus_pentosaceus Pediococcus pentosaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IP6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IP6 FirstGlance]. <br>
-
2IP6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pediococcus_pentosaceus Pediococcus pentosaceus] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IP6 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]] 1.35&#8491;</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>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ip6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ip6 OCA], [https://pdbe.org/2ip6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ip6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ip6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ip6 ProSAT]</span></td></tr>
-
High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins., Kim IK, Kim MK, Kim JH, Yim HS, Cha SS, Kang SO, BMC Struct Biol. 2007 May 30;7:35. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17537233 17537233]
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q79IK2_PEDPE Q79IK2_PEDPE]
 +
== 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/ip/2ip6_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=2ip6 ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Pediococcus pentosaceus]]
[[Category: Pediococcus pentosaceus]]
-
[[Category: Single protein]]
+
[[Category: Cha SS]]
-
[[Category: Cha, S.S.]]
+
[[Category: Kang SO]]
-
[[Category: Kang, S.O.]]
+
[[Category: Kim IK]]
-
[[Category: Kim, I.K.]]
+
[[Category: Kim JH]]
-
[[Category: Kim, J.H.]]
+
[[Category: Kim MK]]
-
[[Category: Kim, M.K.]]
+
[[Category: Yim HS]]
-
[[Category: Yim, H.S.]]
+
-
[[Category: SO4]]
+
-
[[Category: antimicrobial protein]]
+
-
[[Category: immunity protein to the pediocin pp-1]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:17:32 2008''
+

Current revision

Crystal structure of PedB

PDB ID 2ip6

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/2ip6"
Personal tools