2nyd
From Proteopedia
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| - | [[Image:2nyd.gif|left|200px]] | + | [[Image:2nyd.gif|left|200px]] |
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| - | '''Crystal structure of Staphylococcus aureus hypothetical protein SA1388''' | + | {{Structure |
| + | |PDB= 2nyd |SIZE=350|CAPTION= <scene name='initialview01'>2nyd</scene>, resolution 2.00Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= SA1388 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of Staphylococcus aureus hypothetical protein SA1388''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2NYD is a [ | + | 2NYD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYD OCA]. |
==Reference== | ==Reference== | ||
| - | Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center., Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H, BMC Struct Biol. 2006 Dec 23;6:27. PMID:[http:// | + | Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center., Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H, BMC Struct Biol. 2006 Dec 23;6:27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17187687 17187687] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Staphylococcus aureus]] | [[Category: Staphylococcus aureus]] | ||
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[[Category: selenomethionine sad]] | [[Category: selenomethionine sad]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:52:47 2008'' |
Revision as of 15:52, 20 March 2008
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| , resolution 2.00Å | |||||||
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| Ligands: | |||||||
| Gene: | SA1388 (Staphylococcus aureus) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of Staphylococcus aureus hypothetical protein SA1388
Overview
BACKGROUND: The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function. RESULTS: The structure of SA1388 has been solved to 2.0A resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals. It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric "lids" formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site. CONCLUSION: SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The six PII-like domains form two trimeric "lids" that cap the central cavity of the toroid on either side and provide only small openings to allow regulated entry of small molecules into the occluded chamber. The presence of the electron density of the bound ligand may provide important clues on the likely function of NIF3-like proteins.
About this Structure
2NYD is a Single protein structure of sequence from Staphylococcus aureus. Full crystallographic information is available from OCA.
Reference
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center., Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H, BMC Struct Biol. 2006 Dec 23;6:27. PMID:17187687
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