2po3
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:2po3.jpg|left|200px]] | + | [[Image:2po3.jpg|left|200px]] |
| - | + | ||
| - | '''Crystal Structure Analysis of DesI in the presence of its TDP-sugar product''' | + | {{Structure |
| + | |PDB= 2po3 |SIZE=350|CAPTION= <scene name='initialview01'>2po3</scene>, resolution 2.1Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=T4K:(2R,3R,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)IMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL [(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE'>T4K</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= desI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 Streptomyces venezuelae]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure Analysis of DesI in the presence of its TDP-sugar product''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 2PO3 is a [ | + | 2PO3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PO3 OCA]. |
==Reference== | ==Reference== | ||
| - | Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine., Burgie ES, Holden HM, Biochemistry. 2007 Aug 7;46(31):8999-9006. Epub 2007 Jul 13. PMID:[http:// | + | Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine., Burgie ES, Holden HM, Biochemistry. 2007 Aug 7;46(31):8999-9006. Epub 2007 Jul 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17630700 17630700] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Streptomyces venezuelae]] | [[Category: Streptomyces venezuelae]] | ||
| Line 21: | Line 30: | ||
[[Category: tdp-sugar]] | [[Category: tdp-sugar]] | ||
| - | ''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 18:15:25 2008'' |
Revision as of 16:15, 20 March 2008
| |||||||
| , resolution 2.1Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | desI (Streptomyces venezuelae) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure Analysis of DesI in the presence of its TDP-sugar product
Overview
Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found, for example, in such macrolide antibiotics as erthyromycin, azithromycin, and clarithromycin. The efficacies of these macrolide antibiotics are markedly reduced in the absence of desosamine. In the bacterium Streptomyces venezuelae, six enzymes are required for the production of dTDP-desosamine. The focus of this X-ray crystallographic analysis is the third enzyme in the pathway, a PLP-dependent aminotransferase referred to as DesI. The structure of DesI was solved in complex with its product, dTDP-4-amino-4,6-dideoxyglucose, to a nominal resolution of 2.1 A. Each subunit of the dimeric enzyme contains 12 alpha-helices and 14 beta-strands. Three cis-peptides are observed in each subunit, Phe 330, Pro 332, and Pro 339. The two active sites of the enzyme are located in clefts at the subunit/subunit interface. Electron density corresponding to the bound product clearly demonstrates a covalent bond between the amino group of the product and C-4' of the PLP cofactor. Interestingly, there are no hydrogen-bonding interactions between the protein and the dideoxyglucosyl group of the product (within 3.2 A). The only other sugar-modifying aminotransferase whose structure is known in the presence of product is PseC from Helicobacter pylori. This enzyme, as opposed to DesI, catalyzes amino transfer to the axial position of the sugar. A superposition of the two active sites for these proteins reveals that the major differences in ligand binding occur in the orientations of the deoxyglucosyl and phosphoryl groups. Indeed, the nearly 180 degrees difference in hexose orientation explains the equatorial versus axial amino transfer exhibited by DesI and PseC, respectively.
About this Structure
2PO3 is a Single protein structure of sequence from Streptomyces venezuelae. Full crystallographic information is available from OCA.
Reference
Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine., Burgie ES, Holden HM, Biochemistry. 2007 Aug 7;46(31):8999-9006. Epub 2007 Jul 13. PMID:17630700
Page seeded by OCA on Thu Mar 20 18:15:25 2008
