1yhc
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1yhc.gif|left|200px]] | + | [[Image:1yhc.gif|left|200px]] |
| - | + | ||
| - | '''Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate''' | + | {{Structure |
| + | |PDB= 1yhc |SIZE=350|CAPTION= <scene name='initialview01'>1yhc</scene>, resolution 2.10Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PAM:PALMITOLEIC+ACID'>PAM</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= lpxc, envA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1YHC is a [ | + | 1YHC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHC OCA]. |
==Reference== | ==Reference== | ||
| - | UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism., Hernick M, Gennadios HA, Whittington DA, Rusche KM, Christianson DW, Fierke CA, J Biol Chem. 2005 Apr 29;280(17):16969-78. Epub 2005 Feb 10. PMID:[http:// | + | UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism., Hernick M, Gennadios HA, Whittington DA, Rusche KM, Christianson DW, Fierke CA, J Biol Chem. 2005 Apr 29;280(17):16969-78. Epub 2005 Feb 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15705580 15705580] |
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 27: | Line 36: | ||
[[Category: x-ray crystallography; a aeolicus]] | [[Category: x-ray crystallography; a aeolicus]] | ||
| - | ''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 15:22:49 2008'' |
Revision as of 13:22, 20 March 2008
| |||||||
| , resolution 2.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , and | ||||||
| Gene: | lpxc, envA (Aquifex aeolicus) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate
Overview
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a zinc-dependent enzyme that catalyzes the deacetylation of UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to form UDP-3-O-(R-hydroxymyristoyl)glucosamine and acetate. The structural similarity of the active site of LpxC to metalloproteases led to the proposal that LpxC functions via a metalloprotease-like mechanism. The pH dependence of k(cat)/Km catalyzed by Escherichia coli and Aquifex aeolicus LpxC displayed a bell-shaped curve (EcLpxC yields apparent pKa values of 6.4+/-0.1 and 9.1+/-0.1), demonstrating that at least two ionizations are important for maximal activity. Metal substitution and mutagenesis experiments suggest that the basic limb of the pH profile is because of deprotonation of a zinc-coordinated group such as the zinc-water molecule, whereas the acidic limb of the pH profile is caused by protonation of either Glu78 or His265. Furthermore, the magnitude of the activity decreases and synergy observed for the active site mutants suggest that Glu78 and His265 act as a general acid-base catalyst pair. Crystal structures of LpxC complexed with cacodylate or palmitate demonstrate that both Glu78 and His265 hydrogen-bond with the same oxygen atom of the tetrahedral intermediate and the product carboxylate. These structural features suggest that LpxC catalyzes deacetylation by using Glu78 and His265 as a general acid-base pair and the zinc-bound water as a nucleophile.
About this Structure
1YHC is a Single protein structure of sequence from Aquifex aeolicus. Full crystallographic information is available from OCA.
Reference
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism., Hernick M, Gennadios HA, Whittington DA, Rusche KM, Christianson DW, Fierke CA, J Biol Chem. 2005 Apr 29;280(17):16969-78. Epub 2005 Feb 10. PMID:15705580
Page seeded by OCA on Thu Mar 20 15:22:49 2008
Categories: Aquifex aeolicus | Single protein | Christianson, D W. | Fierke, C A. | Gennadios, H A. | Hernick, M. | Rusche, K M. | Whittington, D A. | CAC | CL | GOL | PAM | SO4 | ZN | X-ray crystallography; a aeolicus
