2ip6

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[[Image:2ip6.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of PedB==
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|PDB= 2ip6 |SIZE=350|CAPTION= <scene name='initialview01'>2ip6</scene>, resolution 1.35&Aring;
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<StructureSection load='2ip6' size='340' side='right'caption='[[2ip6]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
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<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>
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|ACTIVITY=
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</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>
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|GENE=
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<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>
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}}
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<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>
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</table>
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'''Crystal structure of PedB'''
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== Function ==
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[https://www.uniprot.org/uniprot/Q79IK2_PEDPE Q79IK2_PEDPE]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/2ip6_consurf.spt"</scriptWhenChecked>
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2IP6 is a [[Single protein]] structure of sequence from [http://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].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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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://www.ncbi.nlm.nih.gov/pubmed/17537233 17537233]
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</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].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pediococcus pentosaceus]]
[[Category: Pediococcus pentosaceus]]
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[[Category: Single protein]]
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[[Category: Cha SS]]
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[[Category: Cha, S S.]]
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[[Category: Kang SO]]
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[[Category: Kang, S O.]]
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[[Category: Kim IK]]
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[[Category: Kim, I K.]]
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[[Category: Kim JH]]
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[[Category: Kim, J H.]]
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[[Category: Kim MK]]
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[[Category: Kim, M K.]]
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[[Category: Yim HS]]
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[[Category: Yim, H S.]]
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[[Category: SO4]]
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[[Category: antimicrobial protein]]
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[[Category: immunity protein to the pediocin pp-1]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:32:04 2008''
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Current revision

Crystal structure of PedB

PDB ID 2ip6

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