2pg8

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[[Image:2pg8.png|left|200px]]
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==Crystal structure of R254K mutanat of DpgC with bound substrate analog==
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<StructureSection load='2pg8' size='340' side='right' caption='[[2pg8]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2pg8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=YE1:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+(3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL+DIHYDROGEN+DIPHOSPHATE'>YE1</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2np9|2np9]]</td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DpgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 Streptomyces toyocaensis])</td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pg8_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The enzyme DpgC belongs to a small class of oxygenases not dependent on accessory cofactors for activity. DpgC is in the biosynthetic pathway for the nonproteinogenic amino acid 3,5-dihydroxyphenylglycine in actinomycetes bacteria responsible for the production of the vancomycin/teicoplanin family of antibiotic natural products. The X-ray structure of DpgC [Widboom, P. W., Fielding, E. N., Liu, Y., and Bruner, S. D. (2007) Nature 447, 342-345] confirmed the absence of cofactors and defined a novel hydrophobic dioxygen binding pocket adjacent to a bound substrate analogue. In this paper, the role specific amino acids play in substrate recognition and catalysis is examined through biochemical and structural characterization of site-specific enzyme mutations and alternate substrates. The results establish the importance of three amino acids, Arg254, Glu299, and Glu189, in the chemistry of DpgC. Arg254 and Glu189 join to form a specific contact with one of the phenolic hydroxyls of the substrate, and this interaction plays a key role in both substrate recognition and catalysis. The X-ray crystal structure of Arg254Lys was determined to address the role this residue plays in the chemistry. In addition, characterization of alternate substrate analogues demonstrates the presence and position of phenol groups are necessary for both enzyme recognition and downstream oxidation chemistry. Overall, this work defines the mechanism of substrate recognition and specificity by the cofactor-independent dioxygenase DpgC.
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{{STRUCTURE_2pg8| PDB=2pg8 | SCENE= }}
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Substrate recognition and catalysis by the cofactor-independent dioxygenase DpgC.,Fielding EN, Widboom PF, Bruner SD Biochemistry. 2007 Dec 11;46(49):13994-4000. Epub 2007 Nov 16. PMID:18004875<ref>PMID:18004875</ref>
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===Crystal structure of R254K mutanat of DpgC with bound substrate analog===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_18004875}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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[[2pg8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA].
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:018004875</ref><references group="xtra"/>
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[[Category: Streptomyces toyocaensis]]
[[Category: Streptomyces toyocaensis]]
[[Category: Fielding, E N.]]
[[Category: Fielding, E N.]]
[[Category: Ligand binding protein]]
[[Category: Ligand binding protein]]
[[Category: Protein-ligand complex]]
[[Category: Protein-ligand complex]]

Revision as of 19:04, 30 September 2014

Crystal structure of R254K mutanat of DpgC with bound substrate analog

2pg8, resolution 3.00Å

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