1m5r: Difference between revisions
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|PDB= 1m5r |SIZE=350|CAPTION= <scene name='initialview01'>1m5r</scene>, resolution 1.8Å | |PDB= 1m5r |SIZE=350|CAPTION= <scene name='initialview01'>1m5r</scene>, resolution 1.8Å | ||
|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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]], [[1ixy|1IXY]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5r OCA], [http://www.ebi.ac.uk/pdbsum/1m5r PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1m5r RCSB]</span> | |||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
1M5R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 1M5R 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=1M5R 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: 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: 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 22:11:38 2008'' | ||
Revision as of 22:11, 30 March 2008
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| , resolution 1.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | BGT (Enterobacteria phage T4) | ||||||
| Activity: | DNA beta-glucosyltransferase, with EC number 2.4.1.27 | ||||||
| Related: | 1JG6, 1IXY
| ||||||
| 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
OverviewOverview
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 StructureAbout this Structure
1M5R is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
ReferenceReference
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
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