2ip6
From Proteopedia
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|PDB= 2ip6 |SIZE=350|CAPTION= <scene name='initialview01'>2ip6</scene>, resolution 1.35Å | |PDB= 2ip6 |SIZE=350|CAPTION= <scene name='initialview01'>2ip6</scene>, resolution 1.35Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene> | + | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ip6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ip6 OCA], [http://www.ebi.ac.uk/pdbsum/2ip6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ip6 RCSB]</span> | ||
}} | }} | ||
| Line 28: | Line 31: | ||
[[Category: Kim, M K.]] | [[Category: Kim, M K.]] | ||
[[Category: Yim, H S.]] | [[Category: Yim, H S.]] | ||
| - | [[Category: SO4]] | ||
[[Category: antimicrobial protein]] | [[Category: antimicrobial protein]] | ||
[[Category: immunity protein to the pediocin pp-1]] | [[Category: immunity protein to the pediocin pp-1]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:47:03 2008'' |
Revision as of 00:47, 31 March 2008
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| , resolution 1.35Å | |||||||
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| Ligands: | |||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of PedB
Overview
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.
About this Structure
2IP6 is a Single protein structure of sequence from Pediococcus pentosaceus. Full crystallographic information is available from OCA.
Reference
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:17537233
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