1slh
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1slh.gif|left|200px]] | + | [[Image:1slh.gif|left|200px]] |
| - | + | ||
| - | '''Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP''' | + | {{Structure |
| + | |PDB= 1slh |SIZE=350|CAPTION= <scene name='initialview01'>1slh</scene>, resolution 3.00Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=DUD:DEOXYURIDINE-5'-DIPHOSPHATE'>DUD</scene> and <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] | ||
| + | |GENE= DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]) | ||
| + | }} | ||
| + | |||
| + | '''Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1SLH is a [ | + | 1SLH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SLH OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism., Chan S, Segelke B, Lekin T, Krupka H, Cho US, Kim MY, So M, Kim CY, Naranjo CM, Rogers YC, Park MS, Waldo GS, Pashkov I, Cascio D, Perry JL, Sawaya MR, J Mol Biol. 2004 Aug 6;341(2):503-17. PMID:[http:// | + | Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism., Chan S, Segelke B, Lekin T, Krupka H, Cho US, Kim MY, So M, Kim CY, Naranjo CM, Rogers YC, Park MS, Waldo GS, Pashkov I, Cascio D, Perry JL, Sawaya MR, J Mol Biol. 2004 Aug 6;341(2):503-17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15276840 15276840] |
[[Category: Mycobacterium tuberculosis]] | [[Category: Mycobacterium tuberculosis]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 40: | Line 49: | ||
[[Category: protein structure initiative]] | [[Category: protein structure initiative]] | ||
[[Category: psi]] | [[Category: psi]] | ||
| - | [[Category: structural | + | [[Category: structural genomic]] |
[[Category: tb structural genomics consortium]] | [[Category: tb structural genomics consortium]] | ||
[[Category: tbsgc]] | [[Category: tbsgc]] | ||
| - | ''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 14:06:31 2008'' |
Revision as of 12:06, 20 March 2008
| |||||||
| , resolution 3.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C (Mycobacterium tuberculosis) | ||||||
| Activity: | dUTP diphosphatase, with EC number 3.6.1.23 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP
Overview
The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.
About this Structure
1SLH is a Single protein structure of sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA.
Reference
Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism., Chan S, Segelke B, Lekin T, Krupka H, Cho US, Kim MY, So M, Kim CY, Naranjo CM, Rogers YC, Park MS, Waldo GS, Pashkov I, Cascio D, Perry JL, Sawaya MR, J Mol Biol. 2004 Aug 6;341(2):503-17. PMID:15276840
Page seeded by OCA on Thu Mar 20 14:06:31 2008
Categories: Mycobacterium tuberculosis | Single protein | DUTP diphosphatase | Cascio, D. | Chan, S. | Cho, U S. | Eisenberg, D. | Kim, C Y. | Kim, M Y. | Krupka, H. | Lekin, T. | Naranjo, C M. | Park, M S. | Pashkov, I. | Perry, J L. | Rogers, Y C. | Sawaya, M R. | Segelke, B. | So, M. | TBSGC, TB Structural Genomics Consortium. | Terwilliger, T C. | Waldo, G S. | Yeates, T O. | DUD | MG | TRS | Jelly-roll | Protein structure initiative | Psi | Structural genomic | Tb structural genomics consortium | Tbsgc
