1y6g
From Proteopedia
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|PDB= 1y6g |SIZE=350|CAPTION= <scene name='initialview01'>1y6g</scene>, resolution 2.8Å | |PDB= 1y6g |SIZE=350|CAPTION= <scene name='initialview01'>1y6g</scene>, resolution 2.8Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=5HU:5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE'>5HU</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=UDP:URIDINE-5'-DIPHOSPHATE'>UDP</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1xv5|1XV5]], [[1y6f|1Y6F]], [[1y8z|1Y8Z]], [[1ya6|1YA6]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6g OCA], [http://www.ebi.ac.uk/pdbsum/1y6g PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1y6g RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1Y6G is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1Y6G 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=1Y6G OCA]. |
==Reference== | ==Reference== | ||
Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase., Lariviere L, Sommer N, Morera S, J Mol Biol. 2005 Sep 9;352(1):139-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16081100 16081100] | Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase., Lariviere L, Sommer N, Morera S, J Mol Biol. 2005 Sep 9;352(1):139-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16081100 16081100] | ||
| - | [[Category: Bacteriophage t4]] | ||
[[Category: DNA alpha-glucosyltransferase]] | [[Category: DNA alpha-glucosyltransferase]] | ||
| + | [[Category: Enterobacteria phage t4]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Lariviere, L.]] | [[Category: Lariviere, L.]] | ||
[[Category: Morera, S.]] | [[Category: Morera, S.]] | ||
[[Category: Sommer, N.]] | [[Category: Sommer, N.]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: EDO]] | ||
| - | [[Category: NCO]] | ||
| - | [[Category: UDP]] | ||
[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:59:23 2008'' |
Revision as of 21:59, 30 March 2008
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| , resolution 2.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , , | ||||||
| Activity: | DNA alpha-glucosyltransferase, with EC number 2.4.1.26 | ||||||
| Related: | 1XV5, 1Y6F, 1Y8Z, 1YA6
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution
Overview
The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose as the sugar donor to form an alpha-glucosidic linkage and a beta-glucosidic linkage, respectively. Five structures of AGT have been determined: a binary complex with the UDP product and four ternary complexes with UDP or UDP-glucose and oligonucleotides containing an A:G, HMU:G (hydroxymethyl uracyl) or AP:G (apurinic/apyrimidinic) mismatch at the target base-pair. AGT adopts the GT-B fold, one of the two folds known for GTs. However, while the sugar donor binding mode is classical for a GT-B enzyme, the sugar acceptor binding mode is unexpected and breaks the established consensus: AGT is the first GT-B enzyme that predominantly binds both the sugar donor and acceptor to the C-terminal domain. Its active site pocket is highly similar to four retaining GT-B glycosyltransferases (trehalose-6-phosphate synthase, glycogen synthase, glycogen and maltodextrin phosphorylases) strongly suggesting a common evolutionary origin and catalytic mechanism for these enzymes. Structure-guided mutagenesis and kinetic analysis do not permit identification of a nucleophile residue responsible for a glycosyl-enzyme intermediate for the classical double displacement mechanism. Interestingly, the DNA structures reveal partially flipped-out bases. They provide evidence for a passive role of AGT in the base-flipping mechanism and for its specific recognition of the acceptor base.
About this Structure
1Y6G is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase., Lariviere L, Sommer N, Morera S, J Mol Biol. 2005 Sep 9;352(1):139-50. PMID:16081100
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