1ixy
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1ixy |SIZE=350|CAPTION= <scene name='initialview01'>1ixy</scene>, resolution 2.5Å | |PDB= 1ixy |SIZE=350|CAPTION= <scene name='initialview01'>1ixy</scene>, resolution 2.5Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=3DR:1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UDP:URIDINE-5'-DIPHOSPHATE'>UDP</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA_beta-glucosyltransferase DNA beta-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.27 2.4.1.27] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_beta-glucosyltransferase DNA beta-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.27 2.4.1.27] </span> |
| - | |GENE= BGT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= BGT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1jg6|1JG6]], [[1m5r|1M5R]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ixy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixy OCA], [http://www.ebi.ac.uk/pdbsum/1ixy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ixy RCSB]</span> | ||
}} | }} | ||
| Line 16: | Line 19: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1IXY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1IXY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IXY OCA]. |
==Reference== | ==Reference== | ||
A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog., Lariviere L, Morera S, J Mol Biol. 2002 Nov 29;324(3):483-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12445783 12445783] | A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog., Lariviere L, Morera S, J Mol Biol. 2002 Nov 29;324(3):483-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12445783 12445783] | ||
| - | [[Category: Bacteriophage t4]] | ||
[[Category: DNA beta-glucosyltransferase]] | [[Category: DNA beta-glucosyltransferase]] | ||
| + | [[Category: Enterobacteria phage t4]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Lariviere, L.]] | [[Category: Lariviere, L.]] | ||
[[Category: Morera, S.]] | [[Category: Morera, S.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: MPD]] | ||
| - | [[Category: UDP]] | ||
[[Category: abasic site]] | [[Category: abasic site]] | ||
[[Category: base-flipping]] | [[Category: base-flipping]] | ||
[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:26:13 2008'' |
Revision as of 18:26, 30 March 2008
| |||||||
| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | BGT (Enterobacteria phage T4) | ||||||
| Activity: | DNA beta-glucosyltransferase, with EC number 2.4.1.27 | ||||||
| Related: | 1JG6, 1M5R
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex
Overview
T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment containing an abasic site. We obtained two crystal structures of a ternary complex BGT-UDP-DNA at 1.8A and 2.5A resolution, one with a Tris molecule and the other with a metal ion at the active site. Both structures reveal a large distortion in the bound DNA. BGT flips the deoxyribose moiety at the abasic site to an extra-helical position and induces a 40 degrees bend in the DNA with a marked widening of the major groove. The Tris molecule mimics the glucose moiety in its transition state. The base-flipping mechanism, which has so far been observed only for glycosylases, methyltransferases and endonucleases, is now reported for a glucosyltransferase. BGT is unique in binding and inserting a loop into the DNA duplex through the major groove only. Furthermore, BGT compresses the backbone DNA one base further than the target base on the 3'-side.
About this Structure
1IXY is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog., Lariviere L, Morera S, J Mol Biol. 2002 Nov 29;324(3):483-90. PMID:12445783
Page seeded by OCA on Sun Mar 30 21:26:13 2008
