1y6h
From Proteopedia
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|PDB= 1y6h |SIZE=350|CAPTION= <scene name='initialview01'>1y6h</scene>, resolution 2.20Å | |PDB= 1y6h |SIZE=350|CAPTION= <scene name='initialview01'>1y6h</scene>, resolution 2.20Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span> |
|GENE= def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 Leptospira interrogans]) | |GENE= def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 Leptospira interrogans]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://www.ebi.ac.uk/pdbsum/1y6h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB]</span> | ||
}} | }} | ||
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[[Category: Song, X.]] | [[Category: Song, X.]] | ||
[[Category: Zhou, Z.]] | [[Category: Zhou, Z.]] | ||
| - | [[Category: FMT]] | ||
| - | [[Category: GLY]] | ||
| - | [[Category: ZN]] | ||
[[Category: open and close conformation]] | [[Category: open and close conformation]] | ||
[[Category: pdf]] | [[Category: pdf]] | ||
| - | ''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 00:59:22 2008'' |
Revision as of 21:59, 30 March 2008
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| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | def (Leptospira interrogans) | ||||||
| Activity: | Peptide deformylase, with EC number 3.5.1.88 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of LIPDF
Overview
Peptide deformylase (PDF), which is essential for normal growth of bacteria but not for higher organisms, is explored as an attractive target for developing novel antibiotics. Here, we present the crystal structure of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our knowledge, this is the first crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66-76) near the active-site pocket adopts "closed" or "open" conformations in the two monomers forming the dimer. In the closed subunit, the CD-loop and residue Arg109 block the entry of the substrate-binding pocket, while the active-site pocket of the open subunit is occupied by the C-terminal tail from the neighbouring molecule. Moreover, a formate group, as one product of deformylisation, is observed bound with the active-site zinc ion. LiPDF displays significant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs.
About this Structure
1Y6H is a Single protein structure of sequence from Leptospira interrogans. This structure supersedes the now removed PDB entry 1RN5. Full crystallographic information is available from OCA.
Reference
Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans., Zhou Z, Song X, Li Y, Gong W, J Mol Biol. 2004 May 21;339(1):207-15. PMID:15123432
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